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Waisman A, Sevlever F, Saulnier D, Francia M, Blanco R, Amín G, Lombardi A, Biani C, Palma MB, Scarafía A, Smucler J, La Greca A, Moro L, Sevlever G, Guberman A, Miriuka S. The transcription factor OCT6 promotes the dissolution of the naïve pluripotent state by repressing Nanog and activating a formative state gene regulatory network. Sci Rep 2024; 14:10420. [PMID: 38710730 PMCID: PMC11074312 DOI: 10.1038/s41598-024-59247-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
In the mouse embryo, the transition from the preimplantation to the postimplantation epiblast is governed by changes in the gene regulatory network (GRN) that lead to transcriptional, epigenetic, and functional changes. This transition can be faithfully recapitulated in vitro by the differentiation of mouse embryonic stem cells (mESCs) to epiblast-like cells (EpiLCs), that reside in naïve and formative states of pluripotency, respectively. However, the GRN that drives this conversion is not fully elucidated. Here we demonstrate that the transcription factor OCT6 is a key driver of this process. Firstly, we show that Oct6 is not expressed in mESCs but is rapidly induced as cells exit the naïve pluripotent state. By deleting Oct6 in mESCs, we find that knockout cells fail to acquire the typical morphological changes associated with the formative state when induced to differentiate. Additionally, the key naïve pluripotency TFs Nanog, Klf2, Nr5a2, Prdm14, and Esrrb were expressed at higher levels than in wild-type cells, indicating an incomplete dismantling of the naïve pluripotency GRN. Conversely, premature expression of Oct6 in naïve cells triggered a rapid morphological transformation mirroring differentiation, that was accompanied by the upregulation of the endogenous Oct6 as well as the formative genes Sox3, Zic2/3, Foxp1, Dnmt3A and FGF5. Strikingly, we found that OCT6 represses Nanog in a bistable manner and that this regulation is at the transcriptional level. Moreover, our findings also reveal that Oct6 is repressed by NANOG. Collectively, our results establish OCT6 as a key TF in the dissolution of the naïve pluripotent state and support a model where Oct6 and Nanog form a double negative feedback loop which could act as an important toggle mediating the transition to the formative state.
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Affiliation(s)
- Ariel Waisman
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina.
| | - Federico Sevlever
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Denisse Saulnier
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Marcos Francia
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Renata Blanco
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Guadalupe Amín
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Antonella Lombardi
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Celeste Biani
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - María Belén Palma
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Agustina Scarafía
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Joaquín Smucler
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Alejandro La Greca
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Lucía Moro
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Gustavo Sevlever
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Alejandra Guberman
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Santiago Miriuka
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina.
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2
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Carvalho S, Zea-Redondo L, Tang TCC, Stachel-Braum P, Miller D, Caldas P, Kukalev A, Diecke S, Grosswendt S, Grosso AR, Pombo A. SRRM2 splicing factor modulates cell fate in early development. Biol Open 2024; 13:bio060415. [PMID: 38656788 PMCID: PMC11070786 DOI: 10.1242/bio.060415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Embryo development is an orchestrated process that relies on tight regulation of gene expression to guide cell differentiation and fate decisions. The Srrm2 splicing factor has recently been implicated in developmental disorders and diseases, but its role in early mammalian development remains unexplored. Here, we show that Srrm2 dosage is critical for maintaining embryonic stem cell pluripotency and cell identity. Srrm2 heterozygosity promotes loss of stemness, characterised by the coexistence of cells expressing naive and formative pluripotency markers, together with extensive changes in gene expression, including genes regulated by serum-response transcription factor (SRF) and differentiation-related genes. Depletion of Srrm2 by RNA interference in embryonic stem cells shows that the earliest effects of Srrm2 heterozygosity are specific alternative splicing events on a small number of genes, followed by expression changes in metabolism and differentiation-related genes. Our findings unveil molecular and cellular roles of Srrm2 in stemness and lineage commitment, shedding light on the roles of splicing regulators in early embryogenesis, developmental diseases and tumorigenesis.
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Affiliation(s)
- Silvia Carvalho
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
- Graduate Program in Areas of Basic and Applied Biology (GABBA), ICBAS, University of Porto, 4050-313 Porto, Portugal
| | - Luna Zea-Redondo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
| | - Tsz Ching Chloe Tang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
| | - Philipp Stachel-Braum
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Exploratory Diagnostic Sciences (EDS) 10178 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), From Cell State to Function Group, 10115 Berlin, Germany
| | - Duncan Miller
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Pluripotent Stem Cells Platform, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany
| | - Paulo Caldas
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Alexander Kukalev
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
| | - Sebastian Diecke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Pluripotent Stem Cells Platform, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany
| | - Stefanie Grosswendt
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Exploratory Diagnostic Sciences (EDS) 10178 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), From Cell State to Function Group, 10115 Berlin, Germany
| | - Ana Rita Grosso
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
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3
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Dehghanian F, Bovio PP, Gather F, Probst S, Naghsh-Nilchi A, Vogel T. ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42, and Dppa3. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119686. [PMID: 38342310 DOI: 10.1016/j.bbamcr.2024.119686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Understanding the genetic underpinnings of protein networks conferring stemness is of broad interest for basic and translational research. METHODS We used multi-omics analyses to identify and characterize stemness genes, and focused on the zinc finger protein 982 (Zfp982) that regulates stemness through the expression of Nanog, Zfp42, and Dppa3 in mouse embryonic stem cells (mESC). RESULTS Zfp982 was expressed in stem cells, and bound to chromatin through a GCAGAGKC motif, for example near the stemness genes Nanog, Zfp42, and Dppa3. Nanog and Zfp42 were direct targets of ZFP982 that decreased in expression upon knockdown and increased upon overexpression of Zfp982. We show that ZFP982 expression strongly correlated with stem cell characteristics, both on the transcriptional and morphological levels. Zfp982 expression decreased with progressive differentiation into ecto-, endo- and mesodermal cell lineages, and knockdown of Zfp982 correlated with morphological and transcriptional features of differentiated cells. Zfp982 showed transcriptional overlap with members of the Hippo signaling pathway, one of which was Yap1, the major co-activator of Hippo signaling. Despite the observation that ZFP982 and YAP1 interacted and localized predominantly to the cytoplasm upon differentiation, the localization of YAP1 was not influenced by ZFP982 localization. CONCLUSIONS Together, our study identified ZFP982 as a transcriptional regulator of early stemness genes, and since ZFP982 is under the control of the Hippo pathway, underscored the importance of the context-dependent Hippo signals for stem cell characteristics.
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Affiliation(s)
- Fariba Dehghanian
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, HezarJarib Street, Isfahan 81746-73441, Iran; Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.
| | - Patrick Piero Bovio
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Fabian Gather
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Simone Probst
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Amirhosein Naghsh-Nilchi
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, HezarJarib Street, Isfahan 81746-73441, Iran
| | - Tanja Vogel
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Centre for Basics in Neuromodulation (Neuromodul Basics), Freiburg, Germany.
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4
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Dillingham CM, Cormaty H, Morgan EC, Tak AI, Esgdaille DE, Boutz PL, Sridharan R. KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.31.543088. [PMID: 37398291 PMCID: PMC10312572 DOI: 10.1101/2023.05.31.543088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cell (ESC) identity is characterized by a lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 family of histone demethylases removes the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find that KDM3A and KDM3B interact with RNA processing factors such as EFTUD2 and PRMT5. Acute selective degradation of the endogenous KDM3A and KDM3B proteins resulted in altered splicing independent of H3K9me2 status or catalytic activity. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12. Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.
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Affiliation(s)
- Caleb M Dillingham
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Harshini Cormaty
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ellen C Morgan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Andrew I Tak
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Dakarai E Esgdaille
- Department of Biochemistry and Biophysics, Center for RNA Biology, Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry
| | - Paul L Boutz
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
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5
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Amiri M, Kiniry SJ, Possemato AP, Mahmood N, Basiri T, Dufour CR, Tabatabaei N, Deng Q, Bellucci MA, Harwalkar K, Stokes MP, Giguère V, Kaufman RJ, Yamanaka Y, Baranov PV, Tahmasebi S, Sonenberg N. Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells. Cell Rep 2024; 43:113615. [PMID: 38159280 PMCID: PMC10962698 DOI: 10.1016/j.celrep.2023.113615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/24/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024] Open
Abstract
The integrated stress response (ISR) is critical for cell survival under stress. In response to diverse environmental cues, eIF2α becomes phosphorylated, engendering a dramatic change in mRNA translation. The activation of ISR plays a pivotal role in the early embryogenesis, but the eIF2-dependent translational landscape in pluripotent embryonic stem cells (ESCs) is largely unexplored. We employ a multi-omics approach consisting of ribosome profiling, proteomics, and metabolomics in wild-type (eIF2α+/+) and phosphorylation-deficient mutant eIF2α (eIF2αA/A) mouse ESCs (mESCs) to investigate phosphorylated (p)-eIF2α-dependent translational control of naive pluripotency. We show a transient increase in p-eIF2α in the naive epiblast layer of E4.5 embryos. Absence of eIF2α phosphorylation engenders an exit from naive pluripotency following 2i (two chemical inhibitors of MEK1/2 and GSK3α/β) withdrawal. p-eIF2α controls translation of mRNAs encoding proteins that govern pluripotency, chromatin organization, and glutathione synthesis. Thus, p-eIF2α acts as a key regulator of the naive pluripotency gene regulatory network.
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Affiliation(s)
- Mehdi Amiri
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, T12 XF62 Cork, Ireland
| | | | - Niaz Mahmood
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Tayebeh Basiri
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Catherine R Dufour
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Negar Tabatabaei
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Qiyun Deng
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Michael A Bellucci
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Keerthana Harwalkar
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Matthew P Stokes
- Cell Signaling Technology, Inc., 3 Trask Lane, Danvers, MA 01923, USA
| | - Vincent Giguère
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Randal J Kaufman
- Degenerative Diseases Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Yojiro Yamanaka
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, T12 XF62 Cork, Ireland
| | - Soroush Tahmasebi
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA.
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada.
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6
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Gökbuget D, Boileau RM, Lenshoek K, Blelloch R. MLL3/MLL4 enzymatic activity shapes DNA replication timing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.569680. [PMID: 38106216 PMCID: PMC10723431 DOI: 10.1101/2023.12.07.569680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Mammalian genomes are replicated in a precise order during S phase, which is cell-type-specific1-3 and correlates with local transcriptional activity2,4-8, chromatin modifications9 and chromatin architecture1,10,11,12. However, the causal relationships between these features and the key regulators of DNA replication timing (RT) are largely unknown. Here, machine learning was applied to quantify chromatin features, including epigenetic marks, histone variants and chromatin architectural factors, best predicting local RT under steady-state and RT changes during early embryonic stem (ES) cell differentiation. About one-third of genome exhibited RT changes during the differentiation. Combined, chromatin features predicted steady-state RT and RT changes with high accuracy. Of these features, histone H3 lysine 4 monomethylation (H3K4me1) catalyzed by MLL3/4 (also known as KMT2C/D) emerged as a top predictor. Loss of Mll3/4 (but not Mll3 alone) or their enzymatic activity resulted in erasure of genome-wide RT dynamics during ES cell differentiation. Sites that normally gain H3K4me1 in a MLL3/4-dependent fashion during the transition failed to transition towards earlier RT, often with transcriptional activation unaffected. Further analysis revealed a requirement for MLL3/4 in promoting DNA replication initiation zones through MCM2 recruitment, providing a direct link for its role in regulating RT. Our results uncover MLL3/4-dependent H3K4me1 as a functional regulator of RT and highlight a causal relationship between the epigenome and RT that is largely uncoupled from transcription. These findings uncover a previously unknown role for MLL3/4-dependent chromatin functions which is likely relevant to the numerous diseases associated with MLL3/4 mutations.
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Affiliation(s)
- Deniz Gökbuget
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Ryan M. Boileau
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Present address: Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Kayla Lenshoek
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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7
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Xiao D, Lin M, Liu C, Geddes TA, Burchfield J, Parker B, Humphrey SJ, Yang P. SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data. NAR Genom Bioinform 2023; 5:lqad099. [PMID: 37954574 PMCID: PMC10632189 DOI: 10.1093/nargab/lqad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/18/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
A major challenge in mass spectrometry-based phosphoproteomics lies in identifying the substrates of kinases, as currently only a small fraction of substrates identified can be confidently linked with a known kinase. Machine learning techniques are promising approaches for leveraging large-scale phosphoproteomics data to computationally predict substrates of kinases. However, the small number of experimentally validated kinase substrates (true positive) and the high data noise in many phosphoproteomics datasets together limit their applicability and utility. Here, we aim to develop advanced kinase-substrate prediction methods to address these challenges. Using a collection of seven large phosphoproteomics datasets, and both traditional and deep learning models, we first demonstrate that a 'pseudo-positive' learning strategy for alleviating small sample size is effective at improving model predictive performance. We next show that a data resampling-based ensemble learning strategy is useful for improving model stability while further enhancing prediction. Lastly, we introduce an ensemble deep learning model ('SnapKin') by incorporating the above two learning strategies into a 'snapshot' ensemble learning algorithm. We propose SnapKin, an ensemble deep learning method, for predicting substrates of kinases from large-scale phosphoproteomics data. We demonstrate that SnapKin consistently outperforms existing methods in kinase-substrate prediction. SnapKin is freely available at https://github.com/PYangLab/SnapKin.
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Affiliation(s)
- Di Xiao
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Michael Lin
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chunlei Liu
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Thomas A Geddes
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Environmental and Life Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - James G Burchfield
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Environmental and Life Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin L Parker
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, Melbourne, VIC 3010, Australia
| | - Sean J Humphrey
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Environmental and Life Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Melbourne, VIC, 3052, Australia
| | - Pengyi Yang
- Computational Systems Biology Group, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
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8
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Francia MG, Verneri P, Oses C, Vazquez Echegaray C, Garcia MR, Toro A, Levi V, Guberman AS. AKT1 induces Nanog promoter in a SUMOylation-dependent manner in different pluripotent contexts. BMC Res Notes 2023; 16:309. [PMID: 37919788 PMCID: PMC10623886 DOI: 10.1186/s13104-023-06598-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023] Open
Abstract
AKT/PKB is a kinase crucial for pluripotency maintenance in pluripotent stem cells. Multiple post-translational modifications modulate its activity. We have previously demonstrated that AKT1 induces the expression of the pluripotency transcription factor Nanog in a SUMOylation-dependent manner in mouse embryonic stem cells. Here, we studied different cellular contexts and main candidates that could mediate this induction. Our results strongly suggest the pluripotency transcription factors OCT4 and SOX2 are not essential mediators. Additionally, we concluded that this induction takes place in different pluripotent contexts but not in terminally differentiated cells. Finally, the cross-matching analysis of ESCs, iPSCs and MEFs transcriptomes and AKT1 phosphorylation targets provided new clues about possible factors that could be involved in the SUMOylation-dependent Nanog induction by AKT.
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Affiliation(s)
- Marcos Gabriel Francia
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Verneri
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Camila Oses
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Camila Vazquez Echegaray
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
- Lund Stem Cell Center, Department of Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
| | - Mora Reneé Garcia
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ayelen Toro
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandra Sonia Guberman
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Laboratorio de Regulación Génica en Células Madre (CONICET-UBA), Intendente Guiraldes 2160 Pab. 2, 4to Piso, QB-71, C1428EGA, Buenos Aires, Argentina.
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9
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Guo G, Yang J, Guo W, Deng H, Yu H, Bai S, Li G, Tang Y, Zhang P, Xu Y, Pan C, Tang Z. Homocysteine impedes neurite outgrowth recovery after intracerebral haemorrhage by downregulating pCAMK2A. Stroke Vasc Neurol 2023; 8:335-348. [PMID: 36854487 PMCID: PMC10512087 DOI: 10.1136/svn-2022-002165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Hyperhomocysteinemia (HHcy) is independently associated with poorer long-term prognosis in patients with intracerebral haemorrhage (ICH); however, the effect and mechanisms of HHcy on ICH are still unclear. Here, we evaluated neurite outgrowth and neurological functional recovery using simulated models of ICH with HHcy in vitro and in vivo. We found that the neurite outgrowth velocity and motor functional recovery in the ICH plus HHcy group were significantly slower than that in the control group, indicating that homocysteine (Hcy) significantly impedes the neurite outgrowth recovery after ICH. Furthermore, phosphoproteomic data and signalome analysis of perihematomal brain tissues suggested that calmodulin-dependent protein kinases 2 (CAMK2A) kinase substrate pairs were significantly downregulated in ICH with HHcy compared with autologous blood injection only, both western blot and immunofluorescence staining confirmed this finding. Additionally, upregulation of pCAMK2A significantly increased neurite outgrowth recovery in ICH with HHcy. Collectively, we clarify the mechanism of HHcy-hindered neurite outgrowth recovery, and pCAMK2A may serve as a therapeutic strategy for promoting neurological recovery after ICH.
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Affiliation(s)
- Guangyu Guo
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jingfei Yang
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenliang Guo
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hong Deng
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Haihan Yu
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuang Bai
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Gaigai Li
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yingxin Tang
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ping Zhang
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, Zhengzhou, China
| | - Chao Pan
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhouping Tang
- Department of Neurology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
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10
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Wang J, Zhang C, Huang Y, Ruan Y, Hu Y, Wang J, Wang F, Yu M, Xu Y, Liu L, Cheng Y, Yang R, Dong Y, Wang J, Yang Y, Xiong J, Tian Y, Gao Q, Zhang J, Jian R. Parallel Genome-Wide CRISPR Screens to Identify State-Dependent Self-Renewal Regulators of Mouse Embryonic Stem Cells. Stem Cells Dev 2023; 32:450-464. [PMID: 37166379 DOI: 10.1089/scd.2023.0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The pluripotency of embryonic stem cells (ESCs) is more accurately viewed as a continuous developmental process rather than a fixed state. However, the factors that play general or state-specific roles in regulating self-renewal in different pluripotency states remain poorly defined. In this study, parallel genome-wide CRISPR/Cas9 knockout (KO) screens were applied in ESCs cultured in the serum plus LIF (SL) and in the 2i plus LIF (2iL) conditions. The candidate genes were classified into seven groups based on their positive or negative effects on self-renewal, and whether this effect was general or state-specific for ESCs under SL and 2iL culture conditions. We characterized the expression and function of genes in these seven groups. The loss of function of novel pluripotent candidate genes Usp28, Zfp598, and Zfp296 was further evaluated in mouse ESCs. Consistent with our screen, the knockout of Usp28 promotes the proliferation of SL-ESCs and 2iL-ESCs, whereas Zfp598 is indispensable for the self-renewal of ESCs under both culture conditions. The cell phenotypes of Zfp296 KO ESCs under SL and 2iL culture conditions were different. Our work provided a valuable resource for dissecting the molecular regulation of ESC self-renewal in different pluripotency states.
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Affiliation(s)
- Jiangjun Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Cell Biology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Chen Zhang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Yan Ruan
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yan Hu
- Department of Military Basic Training and Army Management, Army Health Service Training Base, Army Medical University, Chongqing, China
| | - Jiaqi Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Pathophysiology, College of High-Altitude Military Medicine, Army Medical University, Chongqing, China
| | - Fengsheng Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Meng Yu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Joint Surgery, Southwest Hospital, the First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Yixiao Xu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Lianlian Liu
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yuda Cheng
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Ran Yang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Pathophysiology, College of High-Altitude Military Medicine, Army Medical University, Chongqing, China
| | - Yutong Dong
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
- Department of Military Basic Training and Army Management, Army Health Service Training Base, Army Medical University, Chongqing, China
| | - Jiali Wang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Jiaxiang Xiong
- Experimental Center of Basic Medicine, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yanping Tian
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Qiangguo Gao
- Department of Cell Biology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Junlei Zhang
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Rui Jian
- Laboratory of Stem Cell and Developmental Biology, Department of Histology and Embryology, College of Basic Medical Science, Army Medical University, Chongqing, China
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11
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Zhang H, Ji S, Zhang K, Chen Y, Ming J, Kong F, Wang L, Wang S, Zou Z, Xiong Z, Xu K, Lin Z, Huang B, Liu L, Fan Q, Jin S, Deng H, Xie W. Stable maternal proteins underlie distinct transcriptome, translatome, and proteome reprogramming during mouse oocyte-to-embryo transition. Genome Biol 2023; 24:166. [PMID: 37443062 DOI: 10.1186/s13059-023-02997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The oocyte-to-embryo transition (OET) converts terminally differentiated gametes into a totipotent embryo and is critically controlled by maternal mRNAs and proteins, while the genome is silent until zygotic genome activation. How the transcriptome, translatome, and proteome are coordinated during this critical developmental window remains poorly understood. RESULTS Utilizing a highly sensitive and quantitative mass spectrometry approach, we obtain high-quality proteome data spanning seven mouse stages, from full-grown oocyte (FGO) to blastocyst, using 100 oocytes/embryos at each stage. Integrative analyses reveal distinct proteome reprogramming compared to that of the transcriptome or translatome. FGO to 8-cell proteomes are dominated by FGO-stockpiled proteins, while the transcriptome and translatome are more dynamic. FGO-originated proteins frequently persist to blastocyst while corresponding transcripts are already downregulated or decayed. Improved concordance between protein and translation or transcription is observed for genes starting translation upon meiotic resumption, as well as those transcribed and translated only in embryos. Concordance between protein and transcription/translation is also observed for proteins with short half-lives. We built a kinetic model that predicts protein dynamics by incorporating both initial protein abundance in FGOs and translation kinetics across developmental stages. CONCLUSIONS Through integrative analyses of datasets generated by ultrasensitive methods, our study reveals that the proteome shows distinct dynamics compared to the translatome and transcriptome during mouse OET. We propose that the remarkably stable oocyte-originated proteome may help save resources to accommodate the demanding needs of growing embryos. This study will advance our understanding of mammalian OET and the fundamental principles governing gene expression.
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Affiliation(s)
- Hongmei Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Shuyan Ji
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuling Chen
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jia Ming
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Shun Wang
- School of Mathematics and Statistics, Wuhan University, Wuhan, China
- Hubei Key Laboratory of Computational Science, Wuhan University, Wuhan, China
| | - Zhuoning Zou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Zhuqing Xiong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Bo Huang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou, 310002, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Suoqin Jin
- School of Mathematics and Statistics, Wuhan University, Wuhan, China
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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12
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Wu Y, Sun H, Qin L, Zhang X, Zhou H, Wang Y, Wang L, Li M, Liu J, Zhang J. Human amnion-derived mesenchymal stem cells attenuate acute lung injury in two different acute lung injury mice models. Front Pharmacol 2023; 14:1149659. [PMID: 37388446 PMCID: PMC10304826 DOI: 10.3389/fphar.2023.1149659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 05/25/2023] [Indexed: 07/01/2023] Open
Abstract
Acute lung injury (ALI) is one of the most common clinical emergencies with limited effective pharmaceutical treatment in the clinic, especially when it progresses to acute respiratory distress syndrome (ARDS). Currently, mesenchymal stem cells (MSCs) exhibit specific superiority for ALI/ARDS treatment. However, stem cells from different sources may result in controversial effects on similar disease conditions. This study aimed to determine the effects of human amnion-derived mesenchymal stem cells (hAMSCs) on two different ALI mice model. The administered hAMSCs effectively accumulated in the lung tissues in all hAMSC-treated groups. Compared with the model and 1% human serum albumin (HSA) groups, high-dose hAMSCs (1.0 × 106 cells) group significantly alleviated alveolar-capillary permeability, oxidative stress, inflammatory factors level and histopathological damage. In addition, the NF-κB signaling pathway is one of the key pathways activated during lipopolysaccharide (LPS) or paraquat (PQ)-induced lung injury. Our results indicated that hAMSCs (1.0 × 106 cells) obviously inhibited the expression of p-IKKα/β, p-IκBα, and p-p65 in the lung tissue (p < 0.05). The high-dose (HD) hAMSC treatment exerted beneficial therapeutic effects on ALI mice models without detectable adverse reactions. The therapeutic effect of hAMSCs might involve NF-κB signaling pathway inhibition. hAMSC treatment is a potential candidate therapy for ALI.
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Affiliation(s)
- Yuxuan Wu
- Department of Emergency, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hao Sun
- Department of Emergency, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lianju Qin
- State Key Laboratory of Reproductive Medicine, Center of Clinical Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaomin Zhang
- Department of Emergency, Jiangnan University Medical Center, Wuxi, China
| | - Hao Zhou
- Department of Emergency, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yao Wang
- Department of Emergency, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lumin Wang
- Department of Emergency, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Meng Li
- Department of Emergency, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiayin Liu
- State Key Laboratory of Reproductive Medicine, Center of Clinical Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinsong Zhang
- Department of Emergency, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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13
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Kim T, Kim HJ, Oldfield AJ, Yang P. PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data. STAR Protoc 2023; 4:102203. [PMID: 37000617 PMCID: PMC10090434 DOI: 10.1016/j.xpro.2023.102203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Characterizing transcription factor (TF) genomic colocalization is essential for identifying cooperative binding of TFs in controlling gene expression. Here, we introduce a protocol for using PAD2, an interactive web application that enables the investigation of colocalization of various TFs and chromatin-regulating proteins from mouse embryonic stem cells at various functional genomic regions. We describe steps for accessing and searching the PAD2 database and selecting and submitting genomic regions. We then detail protein colocalization analysis using heatmap and ranked correlation plot. For complete details on the use and execution of this protocol, please refer to Kim et al. (2022).1.
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Affiliation(s)
- Taiyun Kim
- Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; School of Computer Science, Faculty of Engineering, The University of Sydney, Sydney, NSW, Australia.
| | - Hani Jieun Kim
- Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Andrew J Oldfield
- Institut de Génétique Humaine, Université de Montpellier, CNRS-UMR9002, 34000 Montpellier, France
| | - Pengyi Yang
- Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia.
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14
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Arekatla G, Trenzinger C, Reimann A, Loeffler D, Kull T, Schroeder T. Optogenetic manipulation identifies the roles of ERK and AKT dynamics in controlling mouse embryonic stem cell exit from pluripotency. Dev Cell 2023:S1534-5807(23)00183-1. [PMID: 37207652 DOI: 10.1016/j.devcel.2023.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 03/08/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023]
Abstract
ERK and AKT signaling control pluripotent cell self-renewal versus differentiation. ERK pathway activity over time (i.e., dynamics) is heterogeneous between individual pluripotent cells, even in response to the same stimuli. To analyze potential functions of ERK and AKT dynamics in controlling mouse embryonic stem cell (ESC) fates, we developed ESC lines and experimental pipelines for the simultaneous long-term manipulation and quantification of ERK or AKT dynamics and cell fates. We show that ERK activity duration or amplitude or the type of ERK dynamics (e.g., transient, sustained, or oscillatory) alone does not influence exit from pluripotency, but the sum of activity over time does. Interestingly, cells retain memory of previous ERK pulses, with duration of memory retention dependent on duration of previous pulse length. FGF receptor/AKT dynamics counteract ERK-induced pluripotency exit. These findings improve our understanding of how cells integrate dynamics from multiple signaling pathways and translate them into cell fate cues.
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Affiliation(s)
- Geethika Arekatla
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Christoph Trenzinger
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Andreas Reimann
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Dirk Loeffler
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Tobias Kull
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
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15
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Oses C, Francia MG, Verneri P, Vazquez Echegaray C, Guberman AS, Levi V. The dynamical organization of the core pluripotency transcription factors responds to differentiation cues in early S-phase. Front Cell Dev Biol 2023; 11:1125015. [PMID: 37215075 PMCID: PMC10192714 DOI: 10.3389/fcell.2023.1125015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
DNA replication in stem cells is a major challenge for pluripotency preservation and cell fate decisions. This process involves massive changes in the chromatin architecture and the reorganization of many transcription-related molecules in different spatial and temporal scales. Pluripotency is controlled by the master transcription factors (TFs) OCT4, SOX2 and NANOG that partition into condensates in the nucleus of embryonic stem cells. These condensates are proposed to play relevant roles in the regulation of gene expression and the maintenance of pluripotency. Here, we asked whether the dynamical distribution of the pluripotency TFs changes during the cell cycle, particularly during DNA replication. Since the S phase is considered to be a window of opportunity for cell fate decisions, we explored if differentiation cues in G1 phase trigger changes in the distribution of these TFs during the subsequent S phase. Our results show a spatial redistribution of TFs condensates during DNA replication which was not directly related to chromatin compaction. Additionally, fluorescence fluctuation spectroscopy revealed TF-specific, subtle changes in the landscape of TF-chromatin interactions, consistent with their particularities as key players of the pluripotency network. Moreover, we found that differentiation stimuli in the preceding G1 phase triggered a relatively fast and massive reorganization of pluripotency TFs in early-S phase. Particularly, OCT4 and SOX2 condensates dissolved whereas the lifetimes of TF-chromatin interactions increased suggesting that the reorganization of condensates is accompanied with a change in the landscape of TF-chromatin interactions. Notably, NANOG showed impaired interactions with chromatin in stimulated early-S cells in line with its role as naïve pluripotency TF. Together, these findings provide new insights into the regulation of the core pluripotency TFs during DNA replication of embryonic stem cells and highlight their different roles at early differentiation stages.
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Affiliation(s)
- Camila Oses
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marcos Gabriel Francia
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Verneri
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Camila Vazquez Echegaray
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandra Sonia Guberman
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Valeria Levi
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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16
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Carbognin E, Carlini V, Panariello F, Chieregato M, Guerzoni E, Benvegnù D, Perrera V, Malucelli C, Cesana M, Grimaldi A, Mutarelli M, Carissimo A, Tannenbaum E, Kugler H, Hackett JA, Cacchiarelli D, Martello G. Esrrb guides naive pluripotent cells through the formative transcriptional programme. Nat Cell Biol 2023; 25:643-657. [PMID: 37106060 PMCID: PMC7614557 DOI: 10.1038/s41556-023-01131-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/15/2023] [Indexed: 04/29/2023]
Abstract
During embryonic development, naive pluripotent epiblast cells transit to a formative state. The formative epiblast cells form a polarized epithelium, exhibit distinct transcriptional and epigenetic profiles and acquire competence to differentiate into all somatic and germline lineages. However, we have limited understanding of how the transition to a formative state is molecularly controlled. Here we used murine embryonic stem cell models to show that ESRRB is both required and sufficient to activate formative genes. Genetic inactivation of Esrrb leads to illegitimate expression of mesendoderm and extra-embryonic markers, impaired formative expression and failure to self-organize in 3D. Functionally, this results in impaired ability to generate formative stem cells and primordial germ cells in the absence of Esrrb. Computational modelling and genomic analyses revealed that ESRRB occupies key formative genes in naive cells and throughout the formative state. In so doing, ESRRB kickstarts the formative transition, leading to timely and unbiased capacity for multi-lineage differentiation.
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Affiliation(s)
- Elena Carbognin
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Valentina Carlini
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL)-Rome, Adriano Buzzati-Traverso Campus, Rome, Italy
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | | | - Elena Guerzoni
- Department of Biology, University of Padua, Padua, Italy
| | | | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Cristina Malucelli
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, University of Naples 'Federico II', Naples, Italy
| | - Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Margherita Mutarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Istituto di Scienze Applicate e Sistemi Intelligenti 'Eduardo Caianiello', Consiglio Nazionale delle Ricerche, Pozzuoli, Italy
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Istituto per le Applicazioni del Calcolo 'Mauro Picone,' Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Eitan Tannenbaum
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Hillel Kugler
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Jamie A Hackett
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL)-Rome, Adriano Buzzati-Traverso Campus, Rome, Italy.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.
- Department of Translational Medicine, University of Naples 'Federico II', Naples, Italy.
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples 'Federico II', Naples, Italy.
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17
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Glancy E, Wang C, Tuck E, Healy E, Amato S, Neikes HK, Mariani A, Mucha M, Vermeulen M, Pasini D, Bracken AP. PRC2.1- and PRC2.2-specific accessory proteins drive recruitment of different forms of canonical PRC1. Mol Cell 2023; 83:1393-1411.e7. [PMID: 37030288 PMCID: PMC10168607 DOI: 10.1016/j.molcel.2023.03.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 01/19/2023] [Accepted: 03/16/2023] [Indexed: 04/10/2023]
Abstract
Polycomb repressive complex 2 (PRC2) mediates H3K27me3 deposition, which is thought to recruit canonical PRC1 (cPRC1) via chromodomain-containing CBX proteins to promote stable repression of developmental genes. PRC2 forms two major subcomplexes, PRC2.1 and PRC2.2, but their specific roles remain unclear. Through genetic knockout (KO) and replacement of PRC2 subcomplex-specific subunits in naïve and primed pluripotent cells, we uncover distinct roles for PRC2.1 and PRC2.2 in mediating the recruitment of different forms of cPRC1. PRC2.1 catalyzes the majority of H3K27me3 at Polycomb target genes and is sufficient to promote recruitment of CBX2/4-cPRC1 but not CBX7-cPRC1. Conversely, while PRC2.2 is poor at catalyzing H3K27me3, we find that its accessory protein JARID2 is essential for recruitment of CBX7-cPRC1 and the consequent 3D chromatin interactions at Polycomb target genes. We therefore define distinct contributions of PRC2.1- and PRC2.2-specific accessory proteins to Polycomb-mediated repression and uncover a new mechanism for cPRC1 recruitment.
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Affiliation(s)
- Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Cheng Wang
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Ellen Tuck
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Simona Amato
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Hannah K Neikes
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Andrea Mariani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Marlena Mucha
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands; The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Diego Pasini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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18
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Boileau RM, Chen KX, Blelloch R. Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation. Genome Biol 2023; 24:41. [PMID: 36869380 PMCID: PMC9983171 DOI: 10.1186/s13059-023-02883-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/19/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Enhancers are essential in defining cell fates through the control of cell-type-specific gene expression. Enhancer activation is a multi-step process involving chromatin remodelers and histone modifiers including the monomethylation of H3K4 (H3K4me1) by MLL3 (KMT2C) and MLL4 (KMT2D). MLL3/4 are thought to be critical for enhancer activation and cognate gene expression including through the recruitment of acetyltransferases for H3K27. RESULTS Here we test this model by evaluating the impact of MLL3/4 loss on chromatin and transcription during early differentiation of mouse embryonic stem cells. We find that MLL3/4 activity is required at most if not all sites that gain or lose H3K4me1 but is largely dispensable at sites that remain stably methylated during this transition. This requirement extends to H3K27 acetylation (H3K27ac) at most transitional sites. However, many sites gain H3K27ac independent of MLL3/4 or H3K4me1 including enhancers regulating key factors in early differentiation. Furthermore, despite the failure to gain active histone marks at thousands of enhancers, transcriptional activation of nearby genes is largely unaffected, thus uncoupling the regulation of these chromatin events from transcriptional changes during this transition. These data challenge current models of enhancer activation and imply distinct mechanisms between stable and dynamically changing enhancers. CONCLUSIONS Collectively, our study highlights gaps in knowledge about the steps and epistatic relationships of enzymes necessary for enhancer activation and cognate gene transcription.
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Affiliation(s)
- Ryan M. Boileau
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, USA
- Developmental and Stem Cell Biology Graduate Program , University of California San Francisco, San Francisco, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA USA
| | - Kevin X. Chen
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, USA
- Developmental and Stem Cell Biology Graduate Program , University of California San Francisco, San Francisco, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA USA
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19
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Fazakerley DJ, van Gerwen J, Cooke KC, Duan X, Needham EJ, Díaz-Vegas A, Madsen S, Norris DM, Shun-Shion AS, Krycer JR, Burchfield JG, Yang P, Wade MR, Brozinick JT, James DE, Humphrey SJ. Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance. Nat Commun 2023; 14:923. [PMID: 36808134 PMCID: PMC9938909 DOI: 10.1038/s41467-023-36549-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
The failure of metabolic tissues to appropriately respond to insulin ("insulin resistance") is an early marker in the pathogenesis of type 2 diabetes. Protein phosphorylation is central to the adipocyte insulin response, but how adipocyte signaling networks are dysregulated upon insulin resistance is unknown. Here we employ phosphoproteomics to delineate insulin signal transduction in adipocyte cells and adipose tissue. Across a range of insults causing insulin resistance, we observe a marked rewiring of the insulin signaling network. This includes both attenuated insulin-responsive phosphorylation, and the emergence of phosphorylation uniquely insulin-regulated in insulin resistance. Identifying dysregulated phosphosites common to multiple insults reveals subnetworks containing non-canonical regulators of insulin action, such as MARK2/3, and causal drivers of insulin resistance. The presence of several bona fide GSK3 substrates among these phosphosites led us to establish a pipeline for identifying context-specific kinase substrates, revealing widespread dysregulation of GSK3 signaling. Pharmacological inhibition of GSK3 partially reverses insulin resistance in cells and tissue explants. These data highlight that insulin resistance is a multi-nodal signaling defect that includes dysregulated MARK2/3 and GSK3 activity.
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Affiliation(s)
- Daniel J Fazakerley
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Julian van Gerwen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Kristen C Cooke
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Xiaowen Duan
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Elise J Needham
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Alexis Díaz-Vegas
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Søren Madsen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Dougall M Norris
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Amber S Shun-Shion
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - James R Krycer
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, QL, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QL, Australia
| | - James G Burchfield
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Pengyi Yang
- Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW, 2006, Australia
- Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Mark R Wade
- Lilly Research Laboratories, Division of Eli Lilly and Company, Indianapolis, IN, USA
| | - Joseph T Brozinick
- Lilly Research Laboratories, Division of Eli Lilly and Company, Indianapolis, IN, USA
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
- Sydney Medical School, University of Sydney, Sydney, 2006, Australia.
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
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20
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Xiao D, Chen C, Yang P. Computational systems approach towards phosphoproteomics and their downstream regulation. Proteomics 2023; 23:e2200068. [PMID: 35580145 DOI: 10.1002/pmic.202200068] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 11/07/2022]
Abstract
Protein phosphorylation plays an essential role in modulating cell signalling and its downstream transcriptional and translational regulations. Until recently, protein phosphorylation has been studied mostly using low-throughput biochemical assays. The advancement of mass spectrometry (MS)-based phosphoproteomics transformed the field by enabling measurement of proteome-wide phosphorylation events, where tens of thousands of phosphosites are routinely identified and quantified in an experiment. This has brought a significant challenge in analysing large-scale phosphoproteomic data, making computational methods and systems approaches integral parts of phosphoproteomics. Previous works have primarily focused on reviewing the experimental techniques in MS-based phosphoproteomics, yet a systematic survey of the computational landscape in this field is still missing. Here, we review computational methods and tools, and systems approaches that have been developed for phosphoproteomics data analysis. We categorise them into four aspects including data processing, functional analysis, phosphoproteome annotation and their integration with other omics, and in each aspect, we discuss the key methods and example studies. Lastly, we highlight some of the potential research directions on which future work would make a significant contribution to this fast-growing field. We hope this review provides a useful snapshot of the field of computational systems phosphoproteomics and stimulates new research that drives future development.
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Affiliation(s)
- Di Xiao
- Computational Systems Biology Group, Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Carissa Chen
- Computational Systems Biology Group, Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Pengyi Yang
- Computational Systems Biology Group, Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia
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21
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Moutsopoulos I, Williams EC, Mohorianu II. bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data. Brief Bioinform 2023; 24:6965538. [PMID: 36583521 PMCID: PMC9851288 DOI: 10.1093/bib/bbac591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/12/2022] [Accepted: 12/02/2022] [Indexed: 12/31/2022] Open
Abstract
Bulk sequencing experiments (single- and multi-omics) are essential for exploring wide-ranging biological questions. To facilitate interactive, exploratory tasks, coupled with the sharing of easily accessible information, we present bulkAnalyseR, a package integrating state-of-the-art approaches using an expression matrix as the starting point (pre-processing functions are available as part of the package). Static summary images are replaced with interactive panels illustrating quality-checking, differential expression analysis (with noise detection) and biological interpretation (enrichment analyses, identification of expression patterns, followed by inference and comparison of regulatory interactions). bulkAnalyseR can handle different modalities, facilitating robust integration and comparison of cis-, trans- and customised regulatory networks.
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Affiliation(s)
- Ilias Moutsopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
| | - Eleanor C Williams
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
| | - Irina I Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
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22
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Furlan G, Huyghe A, Combémorel N, Lavial F. Molecular versatility during pluripotency progression. Nat Commun 2023; 14:68. [PMID: 36604434 PMCID: PMC9814743 DOI: 10.1038/s41467-022-35775-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
A challenge during development is to ensure lineage segregation while preserving plasticity. Using pluripotency progression as a paradigm, we review how developmental transitions are coordinated by redeployments, rather than global resettings, of cellular components. We highlight how changes in response to extrinsic cues (FGF, WNT, Activin/Nodal, Netrin-1), context- and stoichiometry-dependent action of transcription factors (Oct4, Nanog) and reconfigurations of epigenetic regulators (enhancers, promoters, TrxG, PRC) may confer robustness to naïve to primed pluripotency transition. We propose the notion of Molecular Versatility to regroup mechanisms by which molecules are repurposed to exert different, sometimes opposite, functions in close stem cell configurations.
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Affiliation(s)
- Giacomo Furlan
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.,Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, ON, Canada
| | - Aurélia Huyghe
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Noémie Combémorel
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Fabrice Lavial
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.
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23
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Diaz-Vegas A, Norris DM, Jall-Rogg S, Cooke KC, Conway OJ, Shun-Shion AS, Duan X, Potter M, van Gerwen J, Baird HJ, Humphrey SJ, James DE, Fazakerley DJ, Burchfield JG. A high-content endogenous GLUT4 trafficking assay reveals new aspects of adipocyte biology. Life Sci Alliance 2023; 6:e202201585. [PMID: 36283703 PMCID: PMC9595207 DOI: 10.26508/lsa.202201585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Insulin-induced GLUT4 translocation to the plasma membrane in muscle and adipocytes is crucial for whole-body glucose homeostasis. Currently, GLUT4 trafficking assays rely on overexpression of tagged GLUT4. Here we describe a high-content imaging platform for studying endogenous GLUT4 translocation in intact adipocytes. This method enables high fidelity analysis of GLUT4 responses to specific perturbations, multiplexing of other trafficking proteins and other features including lipid droplet morphology. Using this multiplexed approach we showed that Vps45 and Rab14 are selective regulators of GLUT4, but Trarg1, Stx6, Stx16, Tbc1d4 and Rab10 knockdown affected both GLUT4 and TfR translocation. Thus, GLUT4 and TfR translocation machinery likely have some overlap upon insulin-stimulation. In addition, we identified Kif13A, a Rab10 binding molecular motor, as a novel regulator of GLUT4 traffic. Finally, comparison of endogenous to overexpressed GLUT4 highlights that the endogenous GLUT4 methodology has an enhanced sensitivity to genetic perturbations and emphasises the advantage of studying endogenous protein trafficking for drug discovery and genetic analysis of insulin action in relevant cell types.
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Affiliation(s)
- Alexis Diaz-Vegas
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Dougall M Norris
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Sigrid Jall-Rogg
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Kristen C Cooke
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Olivia J Conway
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Amber S Shun-Shion
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Xiaowen Duan
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Meg Potter
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Julian van Gerwen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Harry Jm Baird
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
- School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Daniel J Fazakerley
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - James G Burchfield
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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24
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Gu Y, Zhou Y, Ju S, Liu X, Zhang Z, Guo J, Gao J, Zang J, Sun H, Chen Q, Wang J, Xu J, Xu Y, Chen Y, Guo Y, Dai J, Ma H, Wang C, Jin G, Li C, Xia Y, Shen H, Yang Y, Guo X, Hu Z. Multi-omics profiling visualizes dynamics of cardiac development and functions. Cell Rep 2022; 41:111891. [PMID: 36577384 DOI: 10.1016/j.celrep.2022.111891] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/14/2022] [Accepted: 12/05/2022] [Indexed: 12/29/2022] Open
Abstract
Cardiogenesis is a tightly regulated dynamic process through a continuum of differentiation and proliferation events. Key factors and pathways governing this process remain incompletely understood. Here, we investigate mice hearts from embryonic day 10.5 to postnatal week 8 and dissect developmental changes in phosphoproteome-, proteome-, metabolome-, and transcriptome-encompassing cardiogenesis and cardiac maturation. We identify mitogen-activated protein kinases as core kinases involved in transcriptional regulation by mediating the phosphorylation of chromatin remodeling proteins during early cardiogenesis. We construct the reciprocal regulatory network of transcription factors (TFs) and identify a series of TFs controlling early cardiogenesis involved in cycling-dependent proliferation. After birth, we identify cardiac resident macrophages with high arachidonic acid metabolism activities likely involved in the clearance of injured apoptotic cardiomyocytes. Together, our comprehensive multi-omics data offer a panoramic view of cardiac development and maturation that provides a resource for further in-depth functional exploration.
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Affiliation(s)
- Yayun Gu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yan Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Sihan Ju
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaofei Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Zicheng Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jia Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jimiao Gao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jie Zang
- School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Hao Sun
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Qi Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jinghan Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Jiani Xu
- School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yiqun Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yingjia Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Juncheng Dai
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Hongxia Ma
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Cheng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Chaojun Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Yang Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211100, China; School of Public Health, Center for Global Health, Nanjing Medical University, Nanjing, Jiangsu 211100, China.
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25
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Williams EC, Chazarra-Gil R, Shahsavari A, Mohorianu I. The Sum of Two Halves May Be Different from the Whole-Effects of Splitting Sequencing Samples Across Lanes. Genes (Basel) 2022; 13:genes13122265. [PMID: 36553532 PMCID: PMC9777937 DOI: 10.3390/genes13122265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
The advances in high-throughput sequencing (HTS) have enabled the characterisation of biological processes at an unprecedented level of detail; most hypotheses in molecular biology rely on analyses of HTS data. However, achieving increased robustness and reproducibility of results remains a main challenge. Although variability in results may be introduced at various stages, e.g., alignment, summarisation or detection of differential expression, one source of variability was systematically omitted: the sequencing design, which propagates through analyses and may introduce an additional layer of technical variation. We illustrate qualitative and quantitative differences arising from splitting samples across lanes on bulk and single-cell sequencing. For bulk mRNAseq data, we focus on differential expression and enrichment analyses; for bulk ChIPseq data, we investigate the effect on peak calling and the peaks' properties. At the single-cell level, we concentrate on identifying cell subpopulations. We rely on markers used for assigning cell identities; both smartSeq and 10× data are presented. The observed reduction in the number of unique sequenced fragments limits the level of detail on which the different prediction approaches depend. Furthermore, the sequencing stochasticity adds in a weighting bias corroborated with variable sequencing depths and (yet unexplained) sequencing bias. Subsequently, we observe an overall reduction in sequencing complexity and a distortion in the biological signal across technologies, experimental contexts, organisms and tissues.
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Affiliation(s)
- Eleanor C. Williams
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Ruben Chazarra-Gil
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Life Sciences-Transcriptomics and Functional Genomics Lab, Barcelona Supercomputing Center (BSC-CNS), 08034 Barcelona, Spain
| | - Arash Shahsavari
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Correspondence:
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26
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Chousal JN, Sohni A, Vitting-Seerup K, Cho K, Kim M, Tan K, Porse B, Wilkinson MF, Cook-Andersen H. Progression of the pluripotent epiblast depends upon the NMD factor UPF2. Development 2022; 149:dev200764. [PMID: 36255229 PMCID: PMC9687065 DOI: 10.1242/dev.200764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that degrades RNAs harboring in-frame stop codons in specific contexts. Loss of NMD factors leads to embryonic lethality in organisms spanning the phylogenetic scale, but the mechanism remains unknown. Here, we report that the core NMD factor, UPF2, is required for expansion of epiblast cells within the inner cell mass of mice in vivo. We identify NMD target mRNAs in mouse blastocysts - both canonical and alternatively processed mRNAs - including those encoding cell cycle arrest and apoptosis factors, raising the possibility that NMD is essential for embryonic cell proliferation and survival. In support, the inner cell mass of Upf2-null blastocysts rapidly regresses with outgrowth and is incompetent for embryonic stem cell derivation in vitro. In addition, we uncovered concordant temporal- and lineage-specific regulation of NMD factors and mRNA targets, indicative of a shift in NMD magnitude during peri-implantation development. Together, our results reveal developmental and molecular functions of the NMD pathway in the early embryo.
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Affiliation(s)
- Jennifer N. Chousal
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Abhishek Sohni
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
- Section for Bioinformatics, Health Technology, Technical University of Denmark (DTU), 2800 Kongens Lyngby, Denmark
| | - Kyucheol Cho
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew Kim
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kun Tan
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Miles F. Wilkinson
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
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27
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Integrative analysis reveals histone demethylase LSD1 promotes RNA polymerase II pausing. iScience 2022; 25:105049. [PMID: 36124234 PMCID: PMC9482124 DOI: 10.1016/j.isci.2022.105049] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/18/2022] [Accepted: 08/26/2022] [Indexed: 11/21/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1) is well-known for its role in decommissioning enhancers during mouse embryonic stem cell (ESC) differentiation. Its role in gene promoters remains poorly understood despite its widespread presence at these sites. Here, we report that LSD1 promotes RNA polymerase II (RNAPII) pausing, a rate-limiting step in transcription regulation, in ESCs. We found the knockdown of LSD1 preferentially affects genes with higher RNAPII pausing. Next, we demonstrate that the co-localization sites of LSD1 and MYC, a factor known to regulate pause-release, are enriched for other RNAPII pausing factors. We show that LSD1 and MYC directly interact and MYC recruitment to genes co-regulated with LSD1 is dependent on LSD1 but not vice versa. The co-regulated gene set is significantly enriched for housekeeping processes and depleted of transcription factors compared to those bound by LSD1 alone. Collectively, our integrative analysis reveals a pleiotropic role of LSD1 in promoting RNAPII pausing. LSD1 promotes RNA polymerase II pausing in mouse embryonic stem cells LSD1 knockdown causes global reduction of RNAPII pausing Co-localized sites of LSD1 and MYC are enriched for RNAPII pausing and releasing factors MYC recruitment to co-regulated genes is dependent on LSD1 but not vice versa
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28
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Galle E, Wong CW, Ghosh A, Desgeorges T, Melrose K, Hinte LC, Castellano-Castillo D, Engl M, de Sousa JA, Ruiz-Ojeda FJ, De Bock K, Ruiz JR, von Meyenn F. H3K18 lactylation marks tissue-specific active enhancers. Genome Biol 2022; 23:207. [PMID: 36192798 PMCID: PMC9531456 DOI: 10.1186/s13059-022-02775-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Background Histone lactylation has been recently described as a novel histone post-translational modification linking cellular metabolism to epigenetic regulation. Results Given the expected relevance of this modification and current limited knowledge of its function, we generate genome-wide datasets of H3K18la distribution in various in vitro and in vivo samples, including mouse embryonic stem cells, macrophages, adipocytes, and mouse and human skeletal muscle. We compare them to profiles of well-established histone modifications and gene expression patterns. Supervised and unsupervised bioinformatics analysis shows that global H3K18la distribution resembles H3K27ac, although we also find notable differences. H3K18la marks active CpG island-containing promoters of highly expressed genes across most tissues assessed, including many housekeeping genes, and positively correlates with H3K27ac and H3K4me3 as well as with gene expression. In addition, H3K18la is enriched at active enhancers that lie in proximity to genes that are functionally important for the respective tissue. Conclusions Overall, our data suggests that H3K18la is not only a marker for active promoters, but also a mark of tissue specific active enhancers. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02775-y.
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Affiliation(s)
- Eva Galle
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Chee-Wai Wong
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Adhideb Ghosh
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Functional Genomics Center Zurich, ETH Zurich and University Zurich, Zurich, Switzerland
| | - Thibaut Desgeorges
- Laboratory of Exercise and Health, Institute of Human Movement Sciences and Sport, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Kate Melrose
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Laura C Hinte
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Daniel Castellano-Castillo
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Magdalena Engl
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Joao Agostinho de Sousa
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Francisco Javier Ruiz-Ojeda
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Center Munich, Neuherberg, 85764, Munich, Germany.,Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain
| | - Katrien De Bock
- Laboratory of Exercise and Health, Institute of Human Movement Sciences and Sport, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Jonatan R Ruiz
- PROFITH (PROmoting FITness and Health through Physical Activity) Research Group, Department of Physical Education and Sport, Faculty of Sport Sciences, University of Granada, Granada, Spain
| | - Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
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29
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Wang Q, Wang Y, Li S, Zhou A, Qin Y. Organelle biogenesis: ribosomes as organizer and performer. Sci Bull (Beijing) 2022; 67:1614-1617. [PMID: 36546035 DOI: 10.1016/j.scib.2022.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Qi Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yibo Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shuoguo Li
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Aoqi Zhou
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Qin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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30
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Abuhashem A, Chivu AG, Zhao Y, Rice EJ, Siepel A, Danko CG, Hadjantonakis AK. RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. Genes Dev 2022; 36:gad.349565.122. [PMID: 35981753 PMCID: PMC9480856 DOI: 10.1101/gad.349565.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/18/2022] [Indexed: 01/03/2023]
Abstract
Promoter-proximal RNA Pol II pausing is a critical step in transcriptional control. Pol II pausing has been predominantly studied in tissue culture systems. While Pol II pausing has been shown to be required for mammalian development, the phenotypic and mechanistic details of this requirement are unknown. Here, we found that loss of Pol II pausing stalls pluripotent state transitions within the epiblast of the early mouse embryo. Using Nelfb -/- mice and a NELFB degron mouse pluripotent stem cell model, we show that embryonic stem cells (ESCs) representing the naïve state of pluripotency successfully initiate a transition program but fail to balance levels of induced and repressed genes and enhancers in the absence of NELF. We found an increase in chromatin-associated NELF during transition from the naïve to later pluripotent states. Overall, our work defines the acute and long-term molecular consequences of NELF loss and reveals a role for Pol II pausing in the pluripotency continuum as a modulator of cell state transitions.
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Affiliation(s)
- Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, New York 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA
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31
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Epigenetics as "conductor" in "orchestra" of pluripotent states. Cell Tissue Res 2022; 390:141-172. [PMID: 35838826 DOI: 10.1007/s00441-022-03667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Pluripotent character is described as the potency of cells to differentiate into all three germ layers. The best example to reinstate the term lies in the context of embryonic stem cells (ESCs). Pluripotent ESC describes the in vitro status of those cells that originate during the complex process of embryogenesis. Pre-implantation to post-implantation development of embryo embrace cells with different levels of stemness. Currently, four states of pluripotency have been recognized, in the progressing order of "naïve," "poised," "formative," and "primed." Epigenetics act as the "conductor" in this "orchestra" of transition in pluripotent states. With a distinguishable gene expression profile, these four states associate with different epigenetic signatures, sometimes distinct while otherwise overlapping. The present review focuses on how epigenetic factors, including DNA methylation, bivalent chromatin, chromatin remodelers, chromatin/nuclear architecture, and microRNA, could dictate pluripotent states and their transition among themselves.
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32
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Ávila-González D, Portillo W, Barragán-Álvarez CP, Hernandez-Montes G, Flores-Garza E, Molina-Hernández A, Diaz-Martinez NE, Diaz NF. The human amniotic epithelium confers a bias to differentiate toward the neuroectoderm lineage in human embryonic stem cells. eLife 2022; 11:68035. [PMID: 35815953 PMCID: PMC9313526 DOI: 10.7554/elife.68035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
Human embryonic stem cells (hESCs) derive from the epiblast and have pluripotent potential. To maintain the conventional conditions of the pluripotent potential in an undifferentiated state, inactivated mouse embryonic fibroblast (iMEF) is used as a feeder layer. However, it has been suggested that hESC under this conventional condition (hESC-iMEF) is an artifact that does not correspond to the in vitro counterpart of the human epiblast. Our previous studies demonstrated the use of an alternative feeder layer of human amniotic epithelial cells (hAECs) to derive and maintain hESC. We wondered if the hESC-hAEC culture could represent a different pluripotent stage than that of naïve or primed conventional conditions, simulating the stage in which the amniotic epithelium derives from the epiblast during peri-implantation. Like the conventional primed hESC-iMEF, hESC-hAEC has the same levels of expression as the ‘pluripotency core’ and does not express markers of naïve pluripotency. However, it presents a downregulation of HOX genes and genes associated with the endoderm and mesoderm, and it exhibits an increase in the expression of ectoderm lineage genes, specifically in the anterior neuroectoderm. Transcriptome analysis showed in hESC-hAEC an upregulated signature of genes coding for transcription factors involved in neural induction and forebrain development, and the ability to differentiate into a neural lineage was superior in comparison with conventional hESC-iMEF. We propose that the interaction of hESC with hAEC confers hESC a biased potential that resembles the anteriorized epiblast, which is predisposed to form the neural ectoderm.
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Affiliation(s)
- Daniela Ávila-González
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | - Wendy Portillo
- Behavioral and Cognitive Neurobiology, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Carla P Barragán-Álvarez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
| | | | - Eliezer Flores-Garza
- Departamento de Biología Molecular y Biotecnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Anayansi Molina-Hernández
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | | | - Nestor F Diaz
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
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33
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Trafficking regulator of GLUT4-1 (TRARG1) is a GSK3 substrate. Biochem J 2022; 479:1237-1256. [PMID: 35594055 PMCID: PMC9284383 DOI: 10.1042/bcj20220153] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 12/19/2022]
Abstract
Trafficking regulator of GLUT4-1, TRARG1, positively regulates insulin-stimulated GLUT4 trafficking and insulin sensitivity. However, the mechanism(s) by which this occurs remain(s) unclear. Using biochemical and mass spectrometry analyses we found that TRARG1 is dephosphorylated in response to insulin in a PI3K/Akt-dependent manner and is a novel substrate for GSK3. Priming phosphorylation of murine TRARG1 at serine 84 allows for GSK3-directed phosphorylation at serines 72, 76 and 80. A similar pattern of phosphorylation was observed in human TRARG1, suggesting that our findings are translatable to human TRARG1. Pharmacological inhibition of GSK3 increased cell surface GLUT4 in cells stimulated with a submaximal insulin dose, and this was impaired following Trarg1 knockdown, suggesting that TRARG1 acts as a GSK3-mediated regulator in GLUT4 trafficking. These data place TRARG1 within the insulin signaling network and provide insights into how GSK3 regulates GLUT4 trafficking in adipocytes.
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Xiao D, Caldow M, Kim HJ, Blazev R, Koopman R, Manandi D, Parker BL, Yang P. Time-resolved Phosphoproteome and Proteome Analysis Reveals Kinase Signalling on Master Transcription Factors During Myogenesis. iScience 2022; 25:104489. [PMID: 35721465 PMCID: PMC9198430 DOI: 10.1016/j.isci.2022.104489] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/14/2022] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
Myogenesis is governed by signaling networks that are tightly regulated in a time-dependent manner. Although different protein kinases have been identified, knowledge of the global signaling networks and their downstream substrates during myogenesis remains incomplete. Here, we map the myogenic differentiation of C2C12 cells using phosphoproteomics and proteomics. From these data, we infer global kinase activity and predict the substrates that are involved in myogenesis. We found that multiple mitogen-activated protein kinases (MAPKs) mark the initial wave of signaling cascades. Further phosphoproteomic and proteomic profiling with MAPK1/3 and MAPK8/9 specific inhibitions unveil their shared and distinctive roles in myogenesis. Lastly, we identified and validated the transcription factor nuclear factor 1 X-type (NFIX) as a novel MAPK1/3 substrate and demonstrated the functional impact of NFIX phosphorylation on myogenesis. Altogether, these data characterize the dynamics, interactions, and downstream control of kinase signaling networks during myogenesis on a global scale. Phosphoproteomic and proteomic maps of myogenic differentiation of C2C12 cells Myogenic kinome activity and kinase-substrates prediction using machine learning MAPK1/3 and MAPK8/9 inhibition unveil shared and distinctive effects on myogenesis Validation of NFIX phosphorylation by MAPK1/3 and its impact on myogenesis
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Affiliation(s)
- Di Xiao
- Computational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marissa Caldow
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hani Jieun Kim
- Computational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ronnie Blazev
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Rene Koopman
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Deborah Manandi
- Computational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Benjamin L. Parker
- Centre for Muscle Research, Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
- Corresponding author
| | - Pengyi Yang
- Computational Systems Biology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
- Corresponding author
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35
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Personalized phosphoproteomics identifies functional signaling. Nat Biotechnol 2022; 40:576-584. [PMID: 34857927 DOI: 10.1038/s41587-021-01099-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/16/2021] [Indexed: 02/07/2023]
Abstract
Protein phosphorylation dynamically integrates environmental and cellular information to control biological processes. Identifying functional phosphorylation amongst the thousands of phosphosites regulated by a perturbation at a global scale is a major challenge. Here we introduce 'personalized phosphoproteomics', a combination of experimental and computational analyses to link signaling with biological function by utilizing human phenotypic variance. We measure individual subject phosphoproteome responses to interventions with corresponding phenotypes measured in parallel. Applying this approach to investigate how exercise potentiates insulin signaling in human skeletal muscle, we identify both known and previously unidentified phosphosites on proteins involved in glucose metabolism. This includes a cooperative relationship between mTOR and AMPK whereby the former directly phosphorylates the latter on S377, for which we find a role in metabolic regulation. These results establish personalized phosphoproteomics as a general approach for investigating the signal transduction underlying complex biology.
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Krumm J, Sekine K, Samaras P, Brazovskaja A, Breunig M, Yasui R, Kleger A, Taniguchi H, Wilhelm M, Treutlein B, Camp JG, Kuster B. High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development. Cell Rep 2022; 38:110604. [PMID: 35354033 DOI: 10.1016/j.celrep.2022.110604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/29/2021] [Accepted: 03/09/2022] [Indexed: 11/29/2022] Open
Abstract
Primary human hepatocytes are widely used to evaluate liver toxicity of drugs, but they are scarce and demanding to culture. Stem cell-derived hepatocytes are increasingly discussed as alternatives. To obtain a better appreciation of the molecular processes during the differentiation of induced pluripotent stem cells into hepatocytes, we employ a quantitative proteomic approach to follow the expression of 9,000 proteins, 12,000 phosphorylation sites, and 800 acetylation sites over time. The analysis reveals stage-specific markers, a major molecular switch between hepatic endoderm versus immature hepatocyte-like cells impacting, e.g., metabolism, the cell cycle, kinase activity, and the expression of drug transporters. Comparing the proteomes of two- (2D) and three-dimensional (3D)-derived hepatocytes with fetal and adult liver indicates a fetal-like status of the in vitro models and lower expression of important ADME/Tox proteins. The collective data enable constructing a molecular roadmap of hepatocyte development that serves as a valuable resource for future research.
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Affiliation(s)
- Johannes Krumm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Keisuke Sekine
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Agnieska Brazovskaja
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Markus Breunig
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany
| | - Ryota Yasui
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan
| | - Alexander Kleger
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan; Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, 4056 Basel, Switzerland
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, 85354 Freising, Germany.
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37
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Xiao D, Kim HJ, Pang I, Yang P. Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities. Bioinformatics 2022; 38:1956-1963. [PMID: 35015814 PMCID: PMC9113330 DOI: 10.1093/bioinformatics/btac015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/21/2021] [Accepted: 01/06/2022] [Indexed: 11/29/2022] Open
Abstract
Motivation The advance of mass spectrometry-based technologies enabled the profiling of the phosphoproteomes of a multitude of cell and tissue types. However, current research primarily focused on investigating the phosphorylation dynamics in specific cell types and experimental conditions, whereas the phosphorylation events that are common across cell/tissue types and stable regardless of experimental conditions are, so far, mostly ignored. Results Here, we developed a statistical framework to identify the stable phosphoproteome across 53 human phosphoproteomics datasets, covering 40 cell/tissue types and 194 conditions/treatments. We demonstrate that the stably phosphorylated sites (SPSs) identified from our statistical framework are evolutionarily conserved, functionally important and enriched in a range of core signaling and gene pathways. Particularly, we show that SPSs are highly enriched in the RNA splicing pathway, an essential cellular process in mammalian cells, and frequently disrupted by cancer mutations, suggesting a link between the dysregulation of RNA splicing and cancer development through mutations on SPSs. Availability and implementation The source code for data analysis in this study is available from Github repository https://github.com/PYangLab/SPSs under the open-source license of GPL-3. The data used in this study are publicly available (see Section 2.8). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Di Xiao
- Computational Systems Biology Group
| | - Hani Jieun Kim
- Computational Systems Biology Group.,Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
| | - Ignatius Pang
- Bioinformatics Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Pengyi Yang
- Computational Systems Biology Group.,Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
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38
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Abuhashem A, Garg V, Hadjantonakis AK. RNA polymerase II pausing in development: orchestrating transcription. Open Biol 2022; 12:210220. [PMID: 34982944 PMCID: PMC8727152 DOI: 10.1098/rsob.210220] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The coordinated regulation of transcriptional networks underpins cellular identity and developmental progression. RNA polymerase II promoter-proximal pausing (Pol II pausing) is a prevalent mechanism by which cells can control and synchronize transcription. Pol II pausing regulates the productive elongation step of transcription at key genes downstream of a variety of signalling pathways, such as FGF and Nodal. Recent advances in our understanding of the Pol II pausing machinery and its role in transcription call for an assessment of these findings within the context of development. In this review, we discuss our current understanding of the molecular basis of Pol II pausing and its function during organismal development. By critically assessing the tools used to study this process we conclude that combining recently developed genomics approaches with refined perturbation systems has the potential to expand our understanding of Pol II pausing mechanistically and functionally in the context of development and beyond.
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Affiliation(s)
- Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA,Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medical College, New York, NY 10021, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medical College, New York, NY 10021, USA
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39
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Sangokoya C. Measuring Endocytosis and Endosomal Uptake at Single Cell Resolution. Methods Mol Biol 2022; 2490:57-67. [PMID: 35486239 DOI: 10.1007/978-1-0716-2281-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Endocytosis impacts many cell biological functions, including in embryonic stem cells (ESCs). It has been shown that endocytosis is necessary for adequate FGF-signaling within the preimplantation ESC to post-implantation epiblast (EpiLC) pluripotency continuum and is required for proper levels of ERK activation. Quantitative methods at single cell resolution are needed to study endocytosis as well as its regulation and roles in these transitioning populations. The methods in this chapter provide an easily adaptable, multiplexable platform to monitor and quantify endosomal uptake at single cell resolution in live cells following receptor-mediated and non-receptor-mediated endocytosis, including nonspecific mechanisms such as pinocytosis.
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Affiliation(s)
- Carolyn Sangokoya
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA.
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40
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Kumar D, Cinghu S, Oldfield AJ, Yang P, Jothi R. Decoding the function of bivalent chromatin in development and cancer. Genome Res 2021; 31:2170-2184. [PMID: 34667120 PMCID: PMC8647824 DOI: 10.1101/gr.275736.121] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/15/2021] [Indexed: 12/12/2022]
Abstract
Bivalent chromatin is characterized by the simultaneous presence of H3K4me3 and H3K27me3, histone modifications generally associated with transcriptionally active and repressed chromatin, respectively. Prevalent in embryonic stem cells (ESCs), bivalency is postulated to poise/prime lineage-controlling developmental genes for rapid activation during embryogenesis while maintaining a transcriptionally repressed state in the absence of activation cues; however, this hypothesis remains to be directly tested. Most gene promoters DNA hypermethylated in adult human cancers are bivalently marked in ESCs, and it was speculated that bivalency predisposes them for aberrant de novo DNA methylation and irreversible silencing in cancer, but evidence supporting this model is largely lacking. Here, we show that bivalent chromatin does not poise genes for rapid activation but protects promoters from de novo DNA methylation. Genome-wide studies in differentiating ESCs reveal that activation of bivalent genes is no more rapid than that of other transcriptionally silent genes, challenging the premise that H3K4me3 is instructive for transcription. H3K4me3 at bivalent promoters-a product of the underlying DNA sequence-persists in nearly all cell types irrespective of gene expression and confers protection from de novo DNA methylation. Bivalent genes in ESCs that are frequent targets of aberrant hypermethylation in cancer are particularly strongly associated with loss of H3K4me3/bivalency in cancer. Altogether, our findings suggest that bivalency protects reversibly repressed genes from irreversible silencing and that loss of H3K4me3 may make them more susceptible to aberrant DNA methylation in diseases such as cancer. Bivalency may thus represent a distinct regulatory mechanism for maintaining epigenetic plasticity.
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Affiliation(s)
- Dhirendra Kumar
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Senthilkumar Cinghu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Andrew J Oldfield
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Pengyi Yang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Raja Jothi
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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41
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Xiao Y, Sosa F, Ross PJ, Diffenderfer KE, Hansen PJ. Regulation of NANOG and SOX2 expression by activin A and a canonical WNT agonist in bovine embryonic stem cells and blastocysts. Biol Open 2021; 10:bio058669. [PMID: 34643229 PMCID: PMC8649639 DOI: 10.1242/bio.058669] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Bovine embryonic stem cells (ESC) have features associated with the primed pluripotent state including low expression of one of the core pluripotency transcription factors, NANOG. It has been reported that NANOG expression can be upregulated in porcine ESC by treatment with activin A and the WNT agonist CHIR99021. Accordingly, it was tested whether expression of NANOG and another pluripotency factor SOX2 could be stimulated by activin A and the WNT agonist CHIR99021. Immunoreactive NANOG and SOX2 were analyzed for bovine ESC lines derived under conditions in which activin A and CHIR99021 were added singly or in combination. Activin A enhanced NANOG expression but also reduced SOX2 expression. CHIR99021 depressed expression of both NANOG and SOX2. In a second experiment, activin A enhanced blastocyst development while CHIR99021 treatment impaired blastocyst formation and reduced number of blastomeres. Activin A treatment decreased blastomeres in the blastocyst that were positive for either NANOG or SOX2 but increased those that were CDX2+ and that were GATA6+ outside the inner cell mass. CHIR99021 reduced SOX2+ and NANOG+ blastomeres without affecting the number or percent of blastomeres that were CDX2+ and GATA6+. Results indicate activation of activin A signaling stimulates NANOG expression during self-renewal of bovine ESC but suppresses cells expressing pluripotency markers in the blastocyst and increases cells expressing CDX2. Actions of activin A to promote blastocyst development may involve its role in promoting trophectoderm formation. Furthermore, results demonstrate the negative role of canonical WNT signaling in cattle for pluripotency marker expression in ESC and in formation of the inner cell mass and epiblast during embryonic development. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Yao Xiao
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
| | - Froylan Sosa
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
| | - Pablo J. Ross
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | | | - Peter J. Hansen
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
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42
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Vega-Sendino M, Olbrich T, Tillo D, Tran AD, Domingo CN, Franco M, FitzGerald PC, Kruhlak MJ, Ruiz S. The ETS transcription factor ERF controls the exit from the naïve pluripotent state in a MAPK-dependent manner. SCIENCE ADVANCES 2021; 7:eabg8306. [PMID: 34597136 DOI: 10.1126/sciadv.abg8306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The naïve epiblast transitions to a pluripotent primed state during embryo implantation. Despite the relevance of the FGF pathway during this period, little is known about the downstream effectors regulating this signaling. Here, we examined the molecular mechanisms coordinating the naïve to primed transition by using inducible ESC to genetically eliminate all RAS proteins. We show that differentiated RASKO ESC remain trapped in an intermediate state of pluripotency with naïve-associated features. Elimination of the transcription factor ERF overcomes the developmental blockage of RAS-deficient cells by naïve enhancer decommissioning. Mechanistically, ERF regulates NANOG expression and ensures naïve pluripotency by strengthening naïve transcription factor binding at ESC enhancers. Moreover, ERF negatively regulates the expression of the methyltransferase DNMT3B, which participates in the extinction of the naïve transcriptional program. Collectively, we demonstrated an essential role for ERF controlling the exit from naïve pluripotency in a MAPK-dependent manner during the progression to primed pluripotency.
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Affiliation(s)
- Maria Vega-Sendino
- Laboratory of Genome Integrity, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Teresa Olbrich
- Laboratory of Genome Integrity, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Desiree Tillo
- Genetics Branch, CCR, NCI, National Institutes of Health, National Institutes of Health, Bethesda, MD, USA
| | - Andy D Tran
- Laboratory of Cancer Biology and Genetics, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Catherine N Domingo
- Laboratory of Genome Integrity, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Mariajose Franco
- Laboratory of Genome Integrity, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Peter C FitzGerald
- Genome Analysis Unit, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Kruhlak
- Laboratory of Cancer Biology and Genetics, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Sergio Ruiz
- Laboratory of Genome Integrity, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
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43
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Enhancer-associated H3K4 methylation safeguards in vitro germline competence. Nat Commun 2021; 12:5771. [PMID: 34599190 PMCID: PMC8486853 DOI: 10.1038/s41467-021-26065-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/16/2021] [Indexed: 01/27/2023] Open
Abstract
Germline specification in mammals occurs through an inductive process whereby competent cells in the post-implantation epiblast differentiate into primordial germ cells (PGC). The intrinsic factors that endow epiblast cells with the competence to respond to germline inductive signals remain unknown. Single-cell RNA sequencing across multiple stages of an in vitro PGC-like cells (PGCLC) differentiation system shows that PGCLC genes initially expressed in the naïve pluripotent stage become homogeneously dismantled in germline competent epiblast like-cells (EpiLC). In contrast, the decommissioning of enhancers associated with these germline genes is incomplete. Namely, a subset of these enhancers partly retain H3K4me1, accumulate less heterochromatic marks and remain accessible and responsive to transcriptional activators. Subsequently, as in vitro germline competence is lost, these enhancers get further decommissioned and lose their responsiveness to transcriptional activators. Importantly, using H3K4me1-deficient cells, we show that the loss of this histone modification reduces the germline competence of EpiLC and decreases PGCLC differentiation efficiency. Our work suggests that, although H3K4me1 might not be essential for enhancer function, it can facilitate the (re)activation of enhancers and the establishment of gene expression programs during specific developmental transitions.
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44
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Matsuzaki F, Uda S, Yamauchi Y, Matsumoto M, Soga T, Maehara K, Ohkawa Y, Nakayama KI, Kuroda S, Kubota H. An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver. Cell Rep 2021; 36:109569. [PMID: 34433063 DOI: 10.1016/j.celrep.2021.109569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/24/2021] [Accepted: 07/29/2021] [Indexed: 12/25/2022] Open
Abstract
An effective combination of multi-omic datasets can enhance our understanding of complex biological phenomena. To build a context-dependent network with multiple omic layers, i.e., a trans-omic network, we perform phosphoproteomics, transcriptomics, proteomics, and metabolomics of murine liver for 4 h after insulin administration and integrate the resulting time series. Structural characteristics and dynamic nature of the network are analyzed to elucidate the impact of insulin. Early and prominent changes in protein phosphorylation and persistent and asynchronous changes in mRNA and protein levels through non-transcriptional mechanisms indicate enhanced crosstalk between phosphorylation-mediated signaling and protein expression regulation. Metabolic response shows different temporal regulation with transient increases at early time points across categories and enhanced response in the amino acid and nucleotide categories at later time points as a result of process convergence. This extensive and dynamic view of the trans-omic network elucidates prominent regulatory mechanisms that drive insulin responses through intricate interlayer coordination.
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Affiliation(s)
- Fumiko Matsuzaki
- Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Shinsuke Uda
- Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yukiyo Yamauchi
- Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, 757 Ichibancho, Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Kazumitsu Maehara
- Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Kubota
- Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.
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Moutsopoulos I, Maischak L, Lauzikaite E, Vasquez Urbina S, Williams E, Drost HG, Mohorianu I. noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise. Nucleic Acids Res 2021; 49:e83. [PMID: 34076236 PMCID: PMC8373073 DOI: 10.1093/nar/gkab433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/16/2021] [Accepted: 05/06/2021] [Indexed: 01/22/2023] Open
Abstract
High-throughput sequencing enables an unprecedented resolution in transcript quantification, at the cost of magnifying the impact of technical noise. The consistent reduction of random background noise to capture functionally meaningful biological signals is still challenging. Intrinsic sequencing variability introducing low-level expression variations can obscure patterns in downstream analyses. We introduce noisyR, a comprehensive noise filter to assess the variation in signal distribution and achieve an optimal information-consistency across replicates and samples; this selection also facilitates meaningful pattern recognition outside the background-noise range. noisyR is applicable to count matrices and sequencing data; it outputs sample-specific signal/noise thresholds and filtered expression matrices. We exemplify the effects of minimizing technical noise on several datasets, across various sequencing assays: coding, non-coding RNAs and interactions, at bulk and single-cell level. An immediate consequence of filtering out noise is the convergence of predictions (differential-expression calls, enrichment analyses and inference of gene regulatory networks) across different approaches.
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Affiliation(s)
- Ilias Moutsopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Lukas Maischak
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 1, 72076 Tübingen, Germany
| | - Elze Lauzikaite
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Sergio A Vasquez Urbina
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 1, 72076 Tübingen, Germany
| | - Eleanor C Williams
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Hajk-Georg Drost
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 1, 72076 Tübingen, Germany
| | - Irina I Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
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Qin W, Ugur E, Mulholland CB, Bultmann S, Solovei I, Modic M, Smets M, Wierer M, Forné I, Imhof A, Cardoso MC, Leonhardt H. Phosphorylation of the HP1β hinge region sequesters KAP1 in heterochromatin and promotes the exit from naïve pluripotency. Nucleic Acids Res 2021; 49:7406-7423. [PMID: 34214177 PMCID: PMC8287961 DOI: 10.1093/nar/gkab548] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin binding protein HP1β plays an important role in chromatin organization and cell differentiation, however the underlying mechanisms remain unclear. Here, we generated HP1β−/− embryonic stem cells and observed reduced heterochromatin clustering and impaired differentiation. We found that during stem cell differentiation, HP1β is phosphorylated at serine 89 by CK2, which creates a binding site for the pluripotency regulator KAP1. This phosphorylation dependent sequestration of KAP1 in heterochromatin compartments causes a downregulation of pluripotency factors and triggers pluripotency exit. Accordingly, HP1β−/− and phospho-mutant cells exhibited impaired differentiation, while ubiquitination-deficient KAP1−/− cells had the opposite phenotype with enhanced differentiation. These results suggest that KAP1 regulates pluripotency via its ubiquitination activity. We propose that the formation of subnuclear membraneless heterochromatin compartments may serve as a dynamic reservoir to trap or release cellular factors. The sequestration of essential regulators defines a novel and active role of heterochromatin in gene regulation and represents a dynamic mode of remote control to regulate cellular processes like cell fate decisions.
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Affiliation(s)
- Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Enes Ugur
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christopher B Mulholland
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Sebastian Bultmann
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Irina Solovei
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London NW1 1AT, United Kingdom
| | - Martha Smets
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
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47
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Yu H, Wang J, Lackford B, Bennett B, Li JL, Hu G. INO80 promotes H2A.Z occupancy to regulate cell fate transition in pluripotent stem cells. Nucleic Acids Res 2021; 49:6739-6755. [PMID: 34139016 DOI: 10.1093/nar/gkab476] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/10/2021] [Accepted: 06/08/2021] [Indexed: 12/27/2022] Open
Abstract
The INO80 chromatin remodeler is involved in many chromatin-dependent cellular functions. However, its role in pluripotency and cell fate transition is not fully defined. We examined the impact of Ino80 deletion in the naïve and primed pluripotent stem cells. We found that Ino80 deletion had minimal effect on self-renewal and gene expression in the naïve state, but led to cellular differentiation and de-repression of developmental genes in the transition toward and maintenance of the primed state. In the naïve state, INO80 pre-marked gene promoters that would adopt bivalent histone modifications by H3K4me3 and H3K27me3 upon transition into the primed state. In the primed state, in contrast to its known role in H2A.Z exchange, INO80 promoted H2A.Z occupancy at these bivalent promoters and facilitated H3K27me3 installation and maintenance as well as downstream gene repression. Together, our results identified an unexpected function of INO80 in H2A.Z deposition and gene regulation. We showed that INO80-dependent H2A.Z occupancy is a critical licensing step for the bivalent domains, and thereby uncovered an epigenetic mechanism by which chromatin remodeling, histone variant deposition and histone modification coordinately control cell fate.
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Affiliation(s)
- Hongyao Yu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Jiajia Wang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Brad Lackford
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Brian Bennett
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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48
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Chaigne A, Smith MB, Lopez Cavestany R, Hannezo E, Chalut KJ, Paluch EK. Three-dimensional geometry controls division symmetry in stem cell colonies. J Cell Sci 2021; 134:jcs255018. [PMID: 34323278 PMCID: PMC8349555 DOI: 10.1242/jcs.255018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell-cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Agathe Chaigne
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Matthew B. Smith
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Rocio Lopez Cavestany
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | | | - Kevin J. Chalut
- Wellcome/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Ewa K. Paluch
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- Wellcome/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
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49
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Pogatzki-Zahn EM, Gomez-Varela D, Erdmann G, Kaschube K, Segelcke D, Schmidt M. A proteome signature for acute incisional pain in dorsal root ganglia of mice. Pain 2021; 162:2070-2086. [PMID: 33492035 PMCID: PMC8208099 DOI: 10.1097/j.pain.0000000000002207] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 12/03/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023]
Abstract
ABSTRACT After surgery, acute pain is still managed insufficiently and may lead to short-term and long-term complications including chronic postsurgical pain and an increased prescription of opioids. Thus, identifying new targets specifically implicated in postoperative pain is of utmost importance to develop effective and nonaddictive analgesics. Here, we used an integrated and multimethod workflow to reveal unprecedented insights into proteome dynamics in dorsal root ganglia (DRG) of mice after plantar incision (INC). Based on a detailed characterization of INC-associated pain-related behavior profiles, including a novel paradigm for nonevoked pain, we performed quantitative mass-spectrometry-based proteomics in DRG 1 day after INC. Our data revealed a hitherto unknown INC-regulated protein signature in DRG with changes in distinct proteins and cellular signaling pathways. In particular, we show the differential regulation of 44 protein candidates, many of which are annotated with pathways related to immune and inflammatory responses such as MAPK/extracellular signal-regulated kinases signaling. Subsequent orthogonal assays comprised multiplex Western blotting, bioinformatic protein network analysis, and immunolabeling in independent mouse cohorts to validate (1) the INC-induced regulation of immune/inflammatory pathways and (2) the high priority candidate Annexin A1. Taken together, our results propose novel potential targets in the context of incision and, therefore, represent a highly valuable resource for further mechanistic and translational studies of postoperative pain.
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Affiliation(s)
- Esther M. Pogatzki-Zahn
- Department of Anaesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - David Gomez-Varela
- Max-Planck Institute of Experimental Medicine, Somatosensory Signaling and Systems Biology Group, Goettingen, Germany
| | | | - Katharina Kaschube
- Department of Anaesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Daniel Segelcke
- Department of Anaesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Manuela Schmidt
- Max-Planck Institute of Experimental Medicine, Somatosensory Signaling and Systems Biology Group, Goettingen, Germany
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50
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Ávila-González D, Portillo W, García-López G, Molina-Hernández A, Díaz-Martínez NE, Díaz NF. Unraveling the Spatiotemporal Human Pluripotency in Embryonic Development. Front Cell Dev Biol 2021; 9:676998. [PMID: 34249929 PMCID: PMC8262797 DOI: 10.3389/fcell.2021.676998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
There have been significant advances in understanding human embryogenesis using human pluripotent stem cells (hPSCs) in conventional monolayer and 3D self-organized cultures. Thus, in vitro models have contributed to elucidate the molecular mechanisms for specification and differentiation during development. However, the molecular and functional spectrum of human pluripotency (i.e., intermediate states, pluripotency subtypes and regionalization) is still not fully understood. This review describes the mechanisms that establish and maintain pluripotency in human embryos and their differences with mouse embryos. Further, it describes a new pluripotent state representing a transition between naïve and primed pluripotency. This review also presents the data that divide pluripotency into substates expressing epiblast regionalization and amnion specification as well as primordial germ cells in primates. Finally, this work analyzes the amnion's relevance as an "signaling center" for regionalization before the onset of gastrulation.
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Affiliation(s)
- Daniela Ávila-González
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Mexico
- Instituto Nacional de Perinatología, Mexico City, Mexico
| | - Wendy Portillo
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | | | | | - Néstor E. Díaz-Martínez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
| | - Néstor F. Díaz
- Instituto Nacional de Perinatología, Mexico City, Mexico
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