1
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Collignon E, Cho B, Furlan G, Fothergill-Robinson J, Martin SB, McClymont SA, Ross RL, Limbach PA, Ramalho-Santos M. m 6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency. Nat Cell Biol 2023; 25:1279-1289. [PMID: 37696947 DOI: 10.1038/s41556-023-01212-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/21/2023] [Indexed: 09/13/2023]
Abstract
Embryos across metazoan lineages can enter reversible states of developmental pausing, or diapause, in response to adverse environmental conditions. The molecular mechanisms that underlie this remarkable dormant state remain largely unknown. Here we show that N6-methyladenosine (m6A) RNA methylation by Mettl3 is required for developmental pausing in mouse blastocysts and embryonic stem (ES) cells. Mettl3 enforces transcriptional dormancy through two interconnected mechanisms: (1) it promotes global mRNA destabilization and (2) it suppresses global nascent transcription by destabilizing the mRNA of the transcriptional amplifier and oncogene N-Myc, which we identify as a crucial anti-pausing factor. Knockdown of N-Myc rescues pausing in Mettl3-/- ES cells, and forced demethylation and stabilization of Mycn mRNA in paused wild-type ES cells largely recapitulates the transcriptional defects of Mettl3-/- ES cells. These findings uncover Mettl3 as a key orchestrator of the crosstalk between transcriptomic and epitranscriptomic regulation during developmental pausing, with implications for dormancy in adult stem cells and cancer.
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Affiliation(s)
- Evelyne Collignon
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC) and Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium.
| | - Brandon Cho
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Giacomo Furlan
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julie Fothergill-Robinson
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sylvia-Bryn Martin
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sarah A McClymont
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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2
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Collignon E, Cho B, Fothergill-Robinson J, Furlan G, Ross RL, Limbach PA, Ramalho-Santos M. m 6 A RNA methylation orchestrates transcriptional dormancy during developmental pausing. bioRxiv 2023:2023.01.30.526234. [PMID: 36778216 PMCID: PMC9915470 DOI: 10.1101/2023.01.30.526234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Embryos across metazoan lineages can enter reversible states of developmental pausing, or diapause, in response to adverse environmental conditions. The molecular mechanisms that underlie this remarkable dormant state remain largely unknown. Here we show that m 6 A RNA methylation by Mettl3 is required for developmental pausing in mice by maintaining dormancy of paused embryonic stem cells and blastocysts. Mettl3 enforces transcriptional dormancy via two interconnected mechanisms: i) it promotes global mRNA destabilization and ii) suppresses global nascent transcription by specifically destabilizing the mRNA of the transcriptional amplifier and oncogene N-Myc, which we identify as a critical anti-pausing factor. Our findings reveal Mettl3 as a key orchestrator of the crosstalk between transcriptomic and epitranscriptomic regulation during pausing, with implications for dormancy in stem cells and cancer.
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Affiliation(s)
- Evelyne Collignon
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto; Toronto, ON M5T 3H7, Canada
| | - Brandon Cho
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto; Toronto, ON M5T 3H7, Canada
| | - Julie Fothergill-Robinson
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto; Toronto, ON M5T 3H7, Canada
| | - Giacomo Furlan
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto; Toronto, ON M5T 3H7, Canada
| | | | - Patrick A. Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati; Cincinnati, OH 45221, USA
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto; Toronto, ON M5T 3H7, Canada
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3
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Kim YK, Cho B, Cook DP, Trcka D, Wrana JL, Ramalho-Santos M. Absolute scaling of single-cell transcriptomes identifies pervasive hypertranscription in adult stem and progenitor cells. Cell Rep 2023; 42:111978. [PMID: 36640358 DOI: 10.1016/j.celrep.2022.111978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 10/27/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Hypertranscription supports biosynthetically demanding cellular states through global transcriptome upregulation. Despite its potential widespread relevance, documented examples of hypertranscription remain few and limited to early development. Here, we demonstrate that absolute scaling of single-cell RNA-sequencing data enables the estimation of total transcript abundances per cell. We validate absolute scaling in known cases of developmental hypertranscription and apply it to adult cell types, revealing a remarkable dynamic range in transcriptional output. In adult organs, hypertranscription marks activated stem/progenitor cells with multilineage potential and is redeployed in conditions of tissue injury, where it precedes bursts of proliferation during regeneration. Our analyses identify a common set of molecular pathways associated with both adult and embryonic hypertranscription, including chromatin remodeling, DNA repair, ribosome biogenesis, and translation. These shared features across diverse cell contexts support hypertranscription as a general and dynamic cellular program that is pervasively employed during development, organ maintenance, and regeneration.
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Affiliation(s)
- Yun-Kyo Kim
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada.
| | - Brandon Cho
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - David P Cook
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada
| | - Dan Trcka
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X5, Canada.
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4
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Abstract
LINE1 is the most active and abundant family of retrotransposons; it is implicated in a number of pathologies, as well as in early embryo development. We present a protocol to specifically knockdown LINE1 in mouse embryonic stem cells and embryos, including details for the nucleofection and zygote microinjection of LINE antisense oligos, followed by RNA FISH validation. This protocol can be used in development, as well as other cell types where LINE1 is believed to be expressed. For complete information on the use and execution of this protocol, please refer to Percharde et al. (2018).
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Affiliation(s)
- Michelle Percharde
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, UK
- Institute of Clinical Sciences (ICS), Imperial College, London W12 0NN, UK
| | - Chih-Jen Lin
- The University of Edinburgh, MRC Centre for Reproductive Health, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto M5T 3H7, Canada
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5
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Bulut-Karslioglu A, Jin H, Kim YK, Cho B, Guzman-Ayala M, Williamson AJK, Hejna M, Stötzel M, Whetton AD, Song JS, Ramalho-Santos M. Chd1 protects genome integrity at promoters to sustain hypertranscription in embryonic stem cells. Nat Commun 2021; 12:4859. [PMID: 34381042 PMCID: PMC8357957 DOI: 10.1038/s41467-021-25088-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/20/2021] [Indexed: 11/09/2022] Open
Abstract
Stem and progenitor cells undergo a global elevation of nascent transcription, or hypertranscription, during key developmental transitions involving rapid cell proliferation. The chromatin remodeler Chd1 mediates hypertranscription in pluripotent cells but its mechanism of action remains poorly understood. Here we report a novel role for Chd1 in protecting genome integrity at promoter regions by preventing DNA double-stranded break (DSB) accumulation in ES cells. Chd1 interacts with several DNA repair factors including Atm, Parp1, Kap1 and Topoisomerase 2β and its absence leads to an accumulation of DSBs at Chd1-bound Pol II-transcribed genes and rDNA. Genes prone to DNA breaks in Chd1 KO ES cells are longer genes with GC-rich promoters, a more labile nucleosomal structure and roles in chromatin regulation, transcription and signaling. These results reveal a vulnerability of hypertranscribing stem cells to accumulation of endogenous DNA breaks, with important implications for developmental and cancer biology.
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Affiliation(s)
- Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Hu Jin
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yun-Kyo Kim
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Brandon Cho
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marcela Guzman-Ayala
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Senti Biosciences, South San Francisco, CA, USA
| | - Andrew J K Williamson
- Stoller Biomarker Discovery Centre, The University of Manchester, Manchester, UK
- Thermo Fisher Scientific, Stafford House, UK
| | - Miroslav Hejna
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | | | - Anthony D Whetton
- Stoller Biomarker Discovery Centre, The University of Manchester, Manchester, UK
| | - Jun S Song
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, IL, USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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6
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Lu JY, Chang L, Li T, Wang T, Yin Y, Zhan G, Han X, Zhang K, Tao Y, Percharde M, Wang L, Peng Q, Yan P, Zhang H, Bi X, Shao W, Hong Y, Wu Z, Ma R, Wang P, Li W, Zhang J, Chang Z, Hou Y, Zhu B, Ramalho-Santos M, Li P, Xie W, Na J, Sun Y, Shen X. Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome. Cell Res 2021; 31:613-630. [PMID: 33514913 PMCID: PMC8169921 DOI: 10.1038/s41422-020-00466-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023] Open
Abstract
Organization of the genome into euchromatin and heterochromatin appears to be evolutionarily conserved and relatively stable during lineage differentiation. In an effort to unravel the basic principle underlying genome folding, here we focus on the genome itself and report a fundamental role for L1 (LINE1 or LINE-1) and B1/Alu retrotransposons, the most abundant subclasses of repetitive sequences, in chromatin compartmentalization. We find that homotypic clustering of L1 and B1/Alu demarcates the genome into grossly exclusive domains, and characterizes and predicts Hi-C compartments. Spatial segregation of L1-rich sequences in the nuclear and nucleolar peripheries and B1/Alu-rich sequences in the nuclear interior is conserved in mouse and human cells and occurs dynamically during the cell cycle. In addition, de novo establishment of L1 and B1 nuclear segregation is coincident with the formation of higher-order chromatin structures during early embryogenesis and appears to be critically regulated by L1 and B1 transcripts. Importantly, depletion of L1 transcripts in embryonic stem cells drastically weakens homotypic repeat contacts and compartmental strength, and disrupts the nuclear segregation of L1- or B1-rich chromosomal sequences at genome-wide and individual sites. Mechanistically, nuclear co-localization and liquid droplet formation of L1 repeat DNA and RNA with heterochromatin protein HP1α suggest a phase-separation mechanism by which L1 promotes heterochromatin compartmentalization. Taken together, we propose a genetically encoded model in which L1 and B1/Alu repeats blueprint chromatin macrostructure. Our model explains the robustness of genome folding into a common conserved core, on which dynamic gene regulation is overlaid across cells.
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Affiliation(s)
- J. Yuyang Lu
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Lei Chang
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, and College of Future Technology, Peking University, Beijing, 100871 China ,grid.508040.9Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, 510005 China
| | - Tong Li
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Ting Wang
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Yafei Yin
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Ge Zhan
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Xue Han
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Ke Zhang
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Yibing Tao
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Michelle Percharde
- grid.14105.310000000122478951MRC London Institute of Medical Sciences (LMS), London, W120NN UK ,grid.7445.20000 0001 2113 8111Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, W120NN UK
| | - Liang Wang
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Qi Peng
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Pixi Yan
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Hui Zhang
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Xianju Bi
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Wen Shao
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Yantao Hong
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Zhongyang Wu
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Runze Ma
- grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Peizhe Wang
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Wenzhi Li
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Jing Zhang
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Zai Chang
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Yingping Hou
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, and College of Future Technology, Peking University, Beijing, 100871 China
| | - Bing Zhu
- grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Miguel Ramalho-Santos
- grid.17063.330000 0001 2157 2938Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, Ontario M5T 3H7 Canada
| | - Pilong Li
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Wei Xie
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Jie Na
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Yujie Sun
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, and College of Future Technology, Peking University, Beijing, 100871 China
| | - Xiaohua Shen
- grid.12527.330000 0001 0662 3178Tsinghua-Peking Joint Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing, 100084 China
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7
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Macrae TA, Ramalho-Santos M. The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development. Nat Commun 2021; 12:1865. [PMID: 33767158 PMCID: PMC7994559 DOI: 10.1038/s41467-021-21910-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Pluripotent cells of the mammalian embryo undergo extensive chromatin rewiring to prepare for lineage commitment after implantation. Repressive H3K27me3, deposited by Polycomb Repressive Complex 2 (PRC2), is reallocated from large blankets in pre-implantation embryos to mark promoters of developmental genes. The regulation of this global redistribution of H3K27me3 is poorly understood. Here we report a post-translational mechanism that destabilizes PRC2 to constrict H3K27me3 during lineage commitment. Using an auxin-inducible degron system, we show that the deubiquitinase Usp9x is required for mouse embryonic stem (ES) cell self-renewal. Usp9x-high ES cells have high PRC2 levels and bear a chromatin and transcriptional signature of the pre-implantation embryo, whereas Usp9x-low ES cells resemble the post-implantation, gastrulating epiblast. We show that Usp9x interacts with, deubiquitinates and stabilizes PRC2. Deletion of Usp9x in post-implantation embryos results in the derepression of genes that normally gain H3K27me3 after gastrulation, followed by the appearance of morphological abnormalities at E9.5, pointing to a recurrent link between Usp9x and PRC2 during development. Usp9x is a marker of "stemness" and is mutated in various neurological disorders and cancers. Our results unveil a Usp9x-PRC2 regulatory axis that is critical at peri-implantation and may be redeployed in other stem cell fate transitions and disease states.
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Affiliation(s)
- Trisha A. Macrae
- grid.266102.10000 0001 2297 6811Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA USA ,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
| | - Miguel Ramalho-Santos
- grid.266102.10000 0001 2297 6811Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA USA ,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
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8
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Rehman SK, Haynes J, Collignon E, Brown KR, Wang Y, Nixon AML, Bruce JP, Wintersinger JA, Singh Mer A, Lo EBL, Leung C, Lima-Fernandes E, Pedley NM, Soares F, McGibbon S, He HH, Pollet A, Pugh TJ, Haibe-Kains B, Morris Q, Ramalho-Santos M, Goyal S, Moffat J, O'Brien CA. Colorectal Cancer Cells Enter a Diapause-like DTP State to Survive Chemotherapy. Cell 2021; 184:226-242.e21. [PMID: 33417860 PMCID: PMC8437243 DOI: 10.1016/j.cell.2020.11.018] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 08/25/2020] [Accepted: 11/10/2020] [Indexed: 12/22/2022]
Abstract
Cancer cells enter a reversible drug-tolerant persister (DTP) state to evade death from chemotherapy and targeted agents. It is increasingly appreciated that DTPs are important drivers of therapy failure and tumor relapse. We combined cellular barcoding and mathematical modeling in patient-derived colorectal cancer models to identify and characterize DTPs in response to chemotherapy. Barcode analysis revealed no loss of clonal complexity of tumors that entered the DTP state and recurred following treatment cessation. Our data fit a mathematical model where all cancer cells, and not a small subpopulation, possess an equipotent capacity to become DTPs. Mechanistically, we determined that DTPs display remarkable transcriptional and functional similarities to diapause, a reversible state of suspended embryonic development triggered by unfavorable environmental conditions. Our study provides insight into how cancer cells use a developmentally conserved mechanism to drive the DTP state, pointing to novel therapeutic opportunities to target DTPs.
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Affiliation(s)
- Sumaiyah K Rehman
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Jennifer Haynes
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Evelyne Collignon
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Yadong Wang
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Allison M L Nixon
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Jeffrey A Wintersinger
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada
| | - Arvind Singh Mer
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Edwyn B L Lo
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Cherry Leung
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Nicholas M Pedley
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Fraser Soares
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sophie McGibbon
- Department of Physics, University of Toronto, Toronto, ON M5S 1A7, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Aaron Pollet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Clinical Genomics Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Quaid Morris
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada; Vector Institute, Toronto, ON M5G 1M1, Canada; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Sidhartha Goyal
- Department of Physics, University of Toronto, Toronto, ON M5S 1A7, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Catherine A O'Brien
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Surgery, University Health Network, Toronto, ON M5G 1L7, Canada.
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9
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Ruggeri E, Lira-Albarrán S, Grow EJ, Liu X, Harner R, Maltepe E, Ramalho-Santos M, Donjacour A, Rinaudo P. Sex-specific epigenetic profile of inner cell mass of mice conceived in vivo or by IVF. Mol Hum Reprod 2020; 26:866-878. [PMID: 33010164 PMCID: PMC7821709 DOI: 10.1093/molehr/gaaa064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
The preimplantation stage of development is exquisitely sensitive to environmental stresses, and changes occurring during this developmental phase may have long-term health effects. Animal studies indicate that IVF offspring display metabolic alterations, including hypertension, glucose intolerance and cardiac hypertrophy, often in a sexual dimorphic fashion. The detailed nature of epigenetic changes following in-vitro culture is, however, unknown. This study was performed to evaluate the epigenetic (using whole-genome bisulfite sequencing (WGBS) and assay for transposase-accessible chromatin using sequencing (ATAC-seq)) and transcriptomic changes (using RNA-seq) occurring in the inner cell mass (ICM) of male or female mouse embryos generated in vivo or by IVF. We found that the ICM of IVF embryos, compared to the in-vivo ICM, differed in 3% of differentially methylated regions (DMRs), of which 0.1% were located on CpG islands. ATAC-seq revealed that 293 regions were more accessible and 101 were less accessible in IVF embryos, while RNA-seq revealed that 21 genes were differentially regulated in IVF embryos. Functional enrichment analysis revealed that stress signalling (STAT and NF-kB signalling), developmental processes and cardiac hypertrophy signalling showed consistent changes in WGBS and ATAC-seq platforms. In contrast, male and female embryos showed minimal changes. Male ICM had an increased number of significantly hyper-methylated DMRs, while only 27 regions showed different chromatin accessibility and only one gene was differentially expressed. In summary, this study provides the first comprehensive analysis of DNA methylation, chromatin accessibility and RNA expression changes induced by IVF in male and female ICMs. This dataset can be of value to all researchers interested in the developmental origin of health and disease (DOHaD) hypothesis and might lead to a better understanding of how early embryonic manipulation may affect adult health.
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Affiliation(s)
- Elena Ruggeri
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
- San Diego Zoo Global, Institute for Conservation Research, Reproductive Sciences, Escondido, CA, 92027, USA
| | - Saúl Lira-Albarrán
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Edward J Grow
- Department of Oncological Sciences and Huntsman Cancer Institute, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Xiaowei Liu
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Royce Harner
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Emin Maltepe
- Department of Pediatrics, University of California, San Francisco, CA, 94143, USA
| | - Miguel Ramalho-Santos
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
- Lunenfeld-Tanenbaum Research Institute, University of Toronto, ON, M5G1X5, Canada
- Department of Molecular Genetics, University of Toronto, ON, M5S1A8, Canada
| | - Annemarie Donjacour
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Paolo Rinaudo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
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10
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Lu JY, Shao W, Chang L, Yin Y, Li T, Zhang H, Hong Y, Percharde M, Guo L, Wu Z, Liu L, Liu W, Yan P, Ramalho-Santos M, Sun Y, Shen X. Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation. Cell Rep 2020; 30:3296-3311.e5. [PMID: 32160538 PMCID: PMC7195444 DOI: 10.1016/j.celrep.2020.02.048] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 11/11/2019] [Accepted: 02/10/2020] [Indexed: 11/06/2022] Open
Abstract
Repetitive elements are abundantly distributed in mammalian genomes. Here, we reveal a striking association between repeat subtypes and gene function. SINE, L1, and low-complexity repeats demarcate distinct functional categories of genes and may dictate the time and level of gene expression by providing binding sites for different regulatory proteins. Importantly, imaging and sequencing analysis show that L1 repeats sequester a large set of genes with specialized functions in nucleolus- and lamina-associated inactive domains that are depleted of SINE repeats. In addition, L1 transcripts bind extensively to its DNA in embryonic stem cells (ESCs). Depletion of L1 RNA in ESCs leads to relocation of L1-enriched chromosomal segments from inactive domains to the nuclear interior and de-repression of L1-associated genes. These results demonstrate a role of L1 DNA and RNA in gene silencing and suggest a general theme of genomic repeats in orchestrating the function, regulation, and expression of their host genes.
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Affiliation(s)
- J Yuyang Lu
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wen Shao
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lei Chang
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Yafei Yin
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tong Li
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hui Zhang
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Michelle Percharde
- MRC London Institute of Medical Sciences (LMS), London W120NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W120NN, UK
| | - Lerui Guo
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhongyang Wu
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lichao Liu
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Liu
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pixi Yan
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON M5T 3H7, Canada
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Xiaohua Shen
- Tsinghua Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China.
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11
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Percharde M, Sultana T, Ramalho-Santos M. What Doesn't Kill You Makes You Stronger: Transposons as Dual Players in Chromatin Regulation and Genomic Variation. Bioessays 2020; 42:e1900232. [PMID: 32053231 DOI: 10.1002/bies.201900232] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/10/2020] [Indexed: 12/22/2022]
Abstract
Transposable elements (TEs) are sequences currently or historically mobile, and are present across all eukaryotic genomes. A growing interest in understanding the regulation and function of TEs has revealed seemingly dichotomous roles for these elements in evolution, development, and disease. On the one hand, many gene regulatory networks owe their organization to the spread of cis-elements and DNA binding sites through TE mobilization during evolution. On the other hand, the uncontrolled activity of transposons can generate mutations and contribute to disease, including cancer, while their increased expression may also trigger immune pathways that result in inflammation or senescence. Interestingly, TEs have recently been found to have novel essential functions during mammalian development. Here, the function and regulation of TEs are discussed, with a focus on LINE1 in mammals. It is proposed that LINE1 is a beneficial endogenous dual regulator of gene expression and genomic diversity during mammalian development, and that both of these functions may be detrimental if deregulated in disease contexts.
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Affiliation(s)
- Michelle Percharde
- MRC London Institute of Medical Sciences (LMS), London, W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Tania Sultana
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5T 3L9, Ontario, Canada
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5T 3L9, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Ontario, Canada
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12
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DiTroia SP, Percharde M, Guerquin MJ, Wall E, Collignon E, Ebata KT, Mesh K, Mahesula S, Agathocleous M, Laird DJ, Livera G, Ramalho-Santos M. Maternal vitamin C regulates reprogramming of DNA methylation and germline development. Nature 2019; 573:271-275. [PMID: 31485074 PMCID: PMC8423347 DOI: 10.1038/s41586-019-1536-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/02/2019] [Indexed: 02/07/2023]
Abstract
Development is often assumed to be hardwired in the genome, but several lines of evidence indicate that it is susceptible to environmental modulation with potential long-term consequences, including in mammals1,2. The embryonic germline is of particular interest because of the potential for intergenerational epigenetic effects. The mammalian germline undergoes extensive DNA demethylation3-7 that occurs in large part by passive dilution of methylation over successive cell divisions, accompanied by active DNA demethylation by TET enzymes3,8-10. TET activity has been shown to be modulated by nutrients and metabolites, such as vitamin C11-15. Here we show that maternal vitamin C is required for proper DNA demethylation and the development of female fetal germ cells in a mouse model. Maternal vitamin C deficiency does not affect overall embryonic development but leads to reduced numbers of germ cells, delayed meiosis and reduced fecundity in adult offspring. The transcriptome of germ cells from vitamin-C-deficient embryos is remarkably similar to that of embryos carrying a null mutation in Tet1. Vitamin C deficiency leads to an aberrant DNA methylation profile that includes incomplete demethylation of key regulators of meiosis and transposable elements. These findings reveal that deficiency in vitamin C during gestation partially recapitulates loss of TET1, and provide a potential intergenerational mechanism for adjusting fecundity to environmental conditions.
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Affiliation(s)
- Stephanie P DiTroia
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle Percharde
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- MRC London Institute of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Marie-Justine Guerquin
- UMR967 INSERM, CEA/DRF/iRCM/SCSR/LDG, Université Paris Diderot, Sorbonne Paris Cité, Université Paris-Sud, Université Paris-Saclay, Laboratory of Development of the Gonads, Fontenay aux Roses, France
| | - Estelle Wall
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Evelyne Collignon
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Kevin T Ebata
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kathryn Mesh
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Swetha Mahesula
- Children's Research Institute and the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michalis Agathocleous
- Children's Research Institute and the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Diana J Laird
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Gabriel Livera
- UMR967 INSERM, CEA/DRF/iRCM/SCSR/LDG, Université Paris Diderot, Sorbonne Paris Cité, Université Paris-Sud, Université Paris-Saclay, Laboratory of Development of the Gonads, Fontenay aux Roses, France
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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13
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Gontier G, Iyer M, Shea JM, Bieri G, Wheatley EG, Ramalho-Santos M, Villeda SA. Tet2 Rescues Age-Related Regenerative Decline and Enhances Cognitive Function in the Adult Mouse Brain. Cell Rep 2019; 22:1974-1981. [PMID: 29466726 PMCID: PMC5870899 DOI: 10.1016/j.celrep.2018.02.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/20/2017] [Accepted: 01/31/2018] [Indexed: 12/21/2022] Open
Abstract
Restoring adult stem cell function provides an exciting approach for rejuvenating the aging brain. However, molecular mechanisms mediating neurogenic rejuvenation remain elusive. Here we report that the enzyme ten eleven translocation methylcytosine dioxygenase 2 (Tet2), which catalyzes the production of 5-hydroxymethylcytosine (5hmC), rescues age-related decline in adult neurogenesis and enhances cognition in mice. We detected a decrease in Tet2 expression and 5hmC levels in the aged hippocampus associated with adult neurogenesis. Mimicking an aged condition in young adults by abrogating Tet2 expression within the hippocampal neurogenic niche, or adult neural stem cells, decreased neurogenesis and impaired learning and memory. In a heterochronic parabiosis rejuvenation model, hippocampal Tet2 expression was restored. Overexpressing Tet2 in the hippocampal neurogenic niche of mature adults increased 5hmC associated with neurogenic processes, offset the precipitous age-related decline in neurogenesis, and enhanced learning and memory. Our data identify Tet2 as a key molecular mediator of neurogenic rejuvenation.
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Affiliation(s)
- Geraldine Gontier
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Manasi Iyer
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeremy M Shea
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gregor Bieri
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elizabeth G Wheatley
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Miguel Ramalho-Santos
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Saul A Villeda
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Physical Therapy and Rehabilitation Science, University of California, San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA.
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14
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Bernstein E, Meissner A, Ramalho-Santos M. Paying PIs from grants blocks talent and diversity. Nature 2018; 563:325. [PMID: 30429558 DOI: 10.1038/d41586-018-07382-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Percharde M, Lin CJ, Yin Y, Guan J, Peixoto GA, Bulut-Karslioglu A, Biechele S, Huang B, Shen X, Ramalho-Santos M. A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity. Cell 2018; 174:391-405.e19. [PMID: 29937225 PMCID: PMC6046266 DOI: 10.1016/j.cell.2018.05.043] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 03/20/2018] [Accepted: 05/17/2018] [Indexed: 01/07/2023]
Abstract
Transposable elements represent nearly half of mammalian genomes and are generally described as parasites, or "junk DNA." The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, yet it is paradoxically highly expressed during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem cells (ESCs) and pre-implantation embryos. In ESCs, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a transcriptional program specific to the 2-cell embryo. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, promoting rRNA synthesis and ESC self-renewal. In embryos, LINE1 RNA is required for Dux silencing, synthesis of rRNA, and exit from the 2-cell stage. The results reveal an essential partnership between LINE1 RNA, Nucleolin, Kap1, and peri-nucleolar chromatin in the regulation of transcription, developmental potency, and ESC self-renewal.
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Affiliation(s)
- Michelle Percharde
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chih-Jen Lin
- The University of Edinburgh, MRC Centre for Reproductive Health, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Yafei Yin
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Juan Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gabriel A Peixoto
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Steffen Biechele
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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16
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Bulut-Karslioglu A, Macrae TA, Oses-Prieto JA, Covarrubias S, Percharde M, Ku G, Diaz A, McManus MT, Burlingame AL, Ramalho-Santos M. The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output. Cell Stem Cell 2018; 22:369-383.e8. [PMID: 29499153 PMCID: PMC5836508 DOI: 10.1016/j.stem.2018.02.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 12/20/2017] [Accepted: 02/07/2018] [Indexed: 10/17/2022]
Abstract
A permissive chromatin environment coupled to hypertranscription drives the rapid proliferation of embryonic stem cells (ESCs) and peri-implantation embryos. We carried out a genome-wide screen to systematically dissect the regulation of the euchromatic state of ESCs. The results revealed that cellular growth pathways, most prominently translation, perpetuate the euchromatic state and hypertranscription of ESCs. Acute inhibition of translation rapidly depletes euchromatic marks in mouse ESCs and blastocysts, concurrent with delocalization of RNA polymerase II and reduction in nascent transcription. Translation inhibition promotes rewiring of chromatin accessibility, which decreases at a subset of active developmental enhancers and increases at histone genes and transposable elements. Proteome-scale analyses revealed that several euchromatin regulators are unstable proteins and continuously depend on a high translational output. We propose that this mechanistic interdependence of euchromatin, transcription, and translation sets the pace of proliferation at peri-implantation and may be employed by other stem/progenitor cells.
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Affiliation(s)
- Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Trisha A Macrae
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, Mass Spectrometry Facility, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sergio Covarrubias
- UCSF Diabetes Center, WM Keck Center for Noncoding RNAs, Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michelle Percharde
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gregory Ku
- UCSF Diabetes Center, WM Keck Center for Noncoding RNAs, Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aaron Diaz
- Department of Neurological Surgery, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael T McManus
- UCSF Diabetes Center, WM Keck Center for Noncoding RNAs, Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, Mass Spectrometry Facility, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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17
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Shenoy TR, Boysen G, Wang MY, Xu QZ, Guo W, Koh FM, Wang C, Zhang LZ, Wang Y, Gil V, Aziz S, Christova R, Rodrigues DN, Crespo M, Rescigno P, Tunariu N, Riisnaes R, Zafeiriou Z, Flohr P, Yuan W, Knight E, Swain A, Ramalho-Santos M, Xu DY, de Bono J, Wu H. CHD1 loss sensitizes prostate cancer to DNA damaging therapy by promoting error-prone double-strand break repair. Ann Oncol 2018; 28:1495-1507. [PMID: 28383660 DOI: 10.1093/annonc/mdx165] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Indexed: 01/08/2023] Open
Abstract
Background Deletion of the chromatin remodeler chromodomain helicase DNA-binding protein 1 (CHD1) is a common genomic alteration found in human prostate cancers (PCas). CHD1 loss represents a distinct PCa subtype characterized by SPOP mutation and higher genomic instability. However, the role of CHD1 in PCa development in vivo and its clinical utility remain unclear. Patients and methods To study the role of CHD1 in PCa development and its loss in clinical management, we generated a genetically engineered mouse model with prostate-specific deletion of murine Chd1 as well as isogenic CHD1 wild-type and homozygous deleted human benign and PCa lines. We also developed patient-derived organoid cultures and screened patients with metastatic PCa for CHD1 loss. Results We demonstrate that CHD1 loss sensitizes cells to DNA damage and causes a synthetic lethal response to DNA damaging therapy in vitro, in vivo, ex vivo, in patient-derived organoid cultures and in a patient with metastatic PCa. Mechanistically, CHD1 regulates 53BP1 stability and CHD1 loss leads to decreased error-free homologous recombination (HR) repair, which is compensated by increased error-prone non-homologous end joining (NHEJ) repair for DNA double-strand break (DSB) repair. Conclusions Our study provides the first in vivo and in patient evidence supporting the role of CHD1 in DSB repair and in response to DNA damaging therapy. We uncover mechanistic insights that CHD1 modulates the choice between HR and NHEJ DSB repair and suggest that CHD1 loss may contribute to the genomic instability seen in this subset of PCas.
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Affiliation(s)
- T R Shenoy
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, USA
| | - G Boysen
- The Institute of Cancer Research, London, UK.,Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - M Y Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Q Z Xu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - W Guo
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - F M Koh
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research and Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, USA
| | - C Wang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, USA
| | - L Z Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Y Wang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, USA
| | - V Gil
- The Institute of Cancer Research, London, UK
| | - S Aziz
- The Institute of Cancer Research, London, UK
| | - R Christova
- The Institute of Cancer Research, London, UK
| | - D N Rodrigues
- The Institute of Cancer Research, London, UK.,Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - M Crespo
- The Institute of Cancer Research, London, UK.,Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - P Rescigno
- Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - N Tunariu
- Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - R Riisnaes
- The Institute of Cancer Research, London, UK.,Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Z Zafeiriou
- Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - P Flohr
- The Institute of Cancer Research, London, UK.,Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - W Yuan
- The Institute of Cancer Research, London, UK
| | - E Knight
- The Institute of Cancer Research, London, UK
| | - A Swain
- The Institute of Cancer Research, London, UK
| | - M Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research and Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, USA
| | - D Y Xu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - J de Bono
- The Institute of Cancer Research, London, UK.,Prostate Cancer Targeted Therapy Group and Drug Development Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - H Wu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, USA.,The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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18
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Ebata KT, Mesh K, Liu S, Bilenky M, Fekete A, Acker MG, Hirst M, Garcia BA, Ramalho-Santos M. Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b. Epigenetics Chromatin 2017; 10:36. [PMID: 28706564 PMCID: PMC5506665 DOI: 10.1186/s13072-017-0143-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 07/03/2017] [Indexed: 01/06/2023] Open
Abstract
Background Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes. Results We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in naïve ES cells. Vitamin C treatment reduces global levels of H3K9me2, but not other histone methylation marks analyzed, as measured by western blot, immunofluorescence and mass spectrometry. Vitamin C leads to widespread loss of H3K9me2 at large chromosomal domains as well as gene promoters and repeat elements. Vitamin C-induced loss of H3K9me2 occurs rapidly within 24 h and is reversible. Importantly, we found that the histone demethylases Kdm3a and Kdm3b are required for vitamin C-induced demethylation of H3K9me2. Moreover, we show that vitamin C-induced Kdm3a/b-mediated H3K9me2 demethylation and Tet-mediated DNA demethylation are independent processes at specific loci. Lastly, we document Kdm3a/b are partially required for the upregulation of germline genes by vitamin C. Conclusions These results reveal a specific role for vitamin C in histone demethylation in ES cells and document that DNA methylation and H3K9me2 cooperate to silence germline genes in pluripotent cells. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0143-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin T Ebata
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA USA
| | - Kathryn Mesh
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA USA
| | - Shichong Liu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Misha Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC Canada
| | | | - Michael G Acker
- Novartis Institutes for Biomedical Research, Cambridge, MA USA
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC Canada.,Department of Microbiology and Immunology, Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC Canada
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA USA
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19
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Percharde M, Bulut-Karslioglu A, Ramalho-Santos M. Hypertranscription in Development, Stem Cells, and Regeneration. Dev Cell 2016; 40:9-21. [PMID: 27989554 DOI: 10.1016/j.devcel.2016.11.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/23/2016] [Accepted: 11/16/2016] [Indexed: 11/29/2022]
Abstract
Cells can globally upregulate their transcriptome during specific transitions, a phenomenon called hypertranscription. Evidence for hypertranscription dates back over 70 years but has gone largely ignored in the genomics era until recently. We discuss data supporting the notion that hypertranscription is a unifying theme in embryonic development, stem cell biology, regeneration, and cell competition. We review the history, methods for analysis, underlying mechanisms, and biological significance of hypertranscription.
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Affiliation(s)
- Michelle Percharde
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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20
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Bulut-Karslioglu A, Biechele S, Jin H, Macrae TA, Hejna M, Gertsenstein M, Song JS, Ramalho-Santos M. Inhibition of mTOR induces a paused pluripotent state. Nature 2016; 540:119-123. [PMID: 27880763 PMCID: PMC5143278 DOI: 10.1038/nature20578] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/01/2016] [Indexed: 01/12/2023]
Abstract
Cultured pluripotent stem cells are a cornerstone of regenerative medicine owing to their ability to give rise to all cell types of the body. Although pluripotent stem cells can be propagated indefinitely in vitro, pluripotency is paradoxically a transient state in vivo, lasting 2-3 days around the time of blastocyst implantation. The exception to this rule is embryonic diapause, a reversible state of suspended development triggered by unfavourable conditions. Diapause is a physiological reproductive strategy widely employed across the animal kingdom, including in mammals, but its regulation remains poorly understood. Here we report that the partial inhibition of mechanistic target of rapamycin (mTOR), a major nutrient sensor and promoter of growth, induces reversible pausing of mouse blastocyst development and allows their prolonged culture ex vivo. Paused blastocysts remain pluripotent and competent-able to give rise to embryonic stem (ES) cells and live, fertile mice. We show that both naturally diapaused blastocysts in vivo and paused blastocysts ex vivo display pronounced reductions in mTOR activity, translation, histone modifications associated with gene activity and transcription. Pausing can be induced directly in cultured ES cells and sustained for weeks without appreciable cell death or deviations from cell cycle distributions. We show that paused ES cells display a remarkable global suppression of transcription, maintain a gene expression signature of diapaused blastocysts and remain pluripotent. These results uncover a new pluripotent stem cell state corresponding to the epiblast of the diapaused blastocyst and indicate that mTOR regulates developmental timing at the peri-implantation stage. Our findings have implications in the fields of assisted reproduction, regenerative medicine, cancer, metabolic disorders and ageing.
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Affiliation(s)
- Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, California 94143, USA
| | - Steffen Biechele
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, California 94143, USA
| | - Hu Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA.,Departments of Bioengineering and Physics, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Trisha A Macrae
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, California 94143, USA
| | - Miroslav Hejna
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA.,Departments of Bioengineering and Physics, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | - Jun S Song
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA.,Departments of Bioengineering and Physics, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, California 94143, USA
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21
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Biechele S, Lin CJ, Rinaudo PF, Ramalho-Santos M. Unwind and transcribe: chromatin reprogramming in the early mammalian embryo. Curr Opin Genet Dev 2015; 34:17-23. [PMID: 26183187 DOI: 10.1016/j.gde.2015.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/30/2015] [Accepted: 06/02/2015] [Indexed: 01/08/2023]
Abstract
Within the first few days of life, the unipotent gametic genomes are rapidly reprogrammed to support emergence of pluripotent cells in the early mammalian embryo. It is now appreciated that this crucial stage of development involves dramatic changes to chromatin at multiple levels, such as DNA methylation, histone modifications, histone mobility, and higher-order chromatin organization. Technological advances are beginning to allow genome-wide views of this chromatin reprogramming, and provide new approaches to functionally dissect its regulation. Here we review recent insights into the dynamic chromatin environment of the early mouse embryo. New data challenge long-held assumptions, for example, with regards to the asymmetry of DNA methylation of the parental genomes or the onset of functional zygotic genome activation. We discuss how impaired chromatin reprogramming can lead to early embryonic lethality, but might also have delayed effects that only manifest later in embryogenesis or postnatally, potentially influencing the propensity for adult-onset diseases.
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Affiliation(s)
- Steffen Biechele
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Chih-Jen Lin
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Paolo F Rinaudo
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Miguel Ramalho-Santos
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA.
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22
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Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M. Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast. Development 2014; 142:118-27. [PMID: 25480920 DOI: 10.1242/dev.114843] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pluripotent mammalian epiblast undergoes unusually fast cell proliferation. This rapid growth is expected to generate a high transcriptional demand, but the underlying mechanisms remain unknown. We show here that the chromatin remodeler Chd1 is required for transcriptional output and development of the mouse epiblast. Chd1(-/-) embryos exhibit proliferation defects and increased apoptosis, are smaller than controls by E5.5 and fail to grow, to become patterned or to gastrulate. Removal of p53 allows progression of Chd1(-/-) mutants only to E7.0-8.0, highlighting the crucial requirement for Chd1 during early post-implantation development. Chd1(-/-) embryonic stem cells (ESCs) have a self-renewal defect and a genome-wide reduction in transcriptional output at both known mRNAs and intergenic transcripts. These transcriptional defects were only uncovered when cell number-normalized approaches were used, and correlate with a lower engagement of RNAP II with transcribed genes in Chd1(-/-) ESCs. We further show that Chd1 directly binds to ribosomal DNA, and that both Chd1(-/-) epiblast cells in vivo and ESCs in vitro express significantly lower levels of ribosomal RNA. In agreement with these findings, mutant cells in vivo and in vitro exhibit smaller and more elongated nucleoli. Thus, the RNA output by both Pol I and II is reduced in Chd1(-/-) cells. Our data indicate that Chd1 promotes a globally elevated transcriptional output required to sustain the distinctly rapid growth of the mouse epiblast.
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Affiliation(s)
- Marcela Guzman-Ayala
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Michael Sachs
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Fong Ming Koh
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Courtney Onodera
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Institute for Human Genetics, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Department of Epidemiology and Biostatistics, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Chih-Jen Lin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Priscilla Wong
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Rachel Nitta
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Jun S Song
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Institute for Human Genetics, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Department of Epidemiology and Biostatistics, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
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23
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Abstract
Genetic screens of an unprecedented scale have recently been made possible by the availability of high-complexity libraries of synthetic oligonucleotides designed to mediate either gene knockdown or gene knockout, coupled with next-generation sequencing. However, several sources of random noise and statistical biases complicate the interpretation of the resulting high-throughput data. We developed HiTSelect, a comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of coverage and integrating relevant metadata. We document the superior performance of HiTSelect using data from both genome-wide RNAi and CRISPR/Cas9 screens. HiTSelect is implemented as an open-source package, with a user-friendly interface for data visualization and pathway exploration. Binary executables are available at http://sourceforge.net/projects/hitselect/, and the source code is available at https://github.com/diazlab/HiTSelect.
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Affiliation(s)
- Aaron A Diaz
- Institute for Human Genetics, University of California, San Francisco, CA, USA The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Han Qin
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA Departments of Obstetrics and Gynecology and Pathology and Center for Reproductive Sciences, University of California, San Francisco, CA, USA Diabetes Center, University of California, San Francisco, CA, USA
| | - Miguel Ramalho-Santos
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA Departments of Obstetrics and Gynecology and Pathology and Center for Reproductive Sciences, University of California, San Francisco, CA, USA Diabetes Center, University of California, San Francisco, CA, USA
| | - Jun S Song
- Institute for Human Genetics, University of California, San Francisco, CA, USA The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
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24
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Qin H, Diaz A, Blouin L, Lebbink RJ, Patena W, Tanbun P, LeProust EM, McManus MT, Song JS, Ramalho-Santos M. Systematic identification of barriers to human iPSC generation. Cell 2014; 158:449-461. [PMID: 25036638 DOI: 10.1016/j.cell.2014.05.040] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 03/05/2014] [Accepted: 05/27/2014] [Indexed: 12/13/2022]
Abstract
Reprogramming of somatic cells to induced pluripotent stem cells (iPSCs) holds enormous promise for regenerative medicine. To elucidate endogenous barriers limiting this process, we systematically dissected human cellular reprogramming by combining a genome-wide RNAi screen, innovative computational methods, extensive single-hit validation, and mechanistic investigation of relevant pathways and networks. We identify reprogramming barriers, including genes involved in transcription, chromatin regulation, ubiquitination, dephosphorylation, vesicular transport, and cell adhesion. Specific a disintegrin and metalloproteinase (ADAM) proteins inhibit reprogramming, and the disintegrin domain of ADAM29 is necessary and sufficient for this function. Clathrin-mediated endocytosis can be targeted with small molecules and opposes reprogramming by positively regulating TGF-β signaling. Genetic interaction studies of endocytosis or ubiquitination reveal that barrier pathways can act in linear, parallel, or feedforward loop architectures to antagonize reprogramming. These results provide a global view of barriers to human cellular reprogramming.
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Affiliation(s)
- Han Qin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Ob/Gyn and Pathology, Center for Reproductive Sciences, and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aaron Diaz
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laure Blouin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Ob/Gyn and Pathology, Center for Reproductive Sciences, and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert Jan Lebbink
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, Diabetes Center, and the WM Keck Center for Noncoding RNAs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Weronika Patena
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, Diabetes Center, and the WM Keck Center for Noncoding RNAs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Priscilia Tanbun
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Ob/Gyn and Pathology, Center for Reproductive Sciences, and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily M LeProust
- Genomics Solution Unit, Agilent Technologies Inc., Santa Clara, CA 95051, USA
| | - Michael T McManus
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, Diabetes Center, and the WM Keck Center for Noncoding RNAs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jun S Song
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Ob/Gyn and Pathology, Center for Reproductive Sciences, and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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25
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Lin CJ, Koh FM, Wong P, Conti M, Ramalho-Santos M. Hira-mediated H3.3 incorporation is required for DNA replication and ribosomal RNA transcription in the mouse zygote. Dev Cell 2014; 30:268-79. [PMID: 25087892 DOI: 10.1016/j.devcel.2014.06.022] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 05/09/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
Abstract
Extensive chromatin reprogramming occurs at fertilization and is thought to be under the control of maternal factors, but the underlying mechanisms remain poorly understood. We report that maternal Hira, a chaperone for the histone variant H3.3, is required for mouse development past the zygote stage. Male pronucleus formation is inhibited upon deletion of Hira due to a lack of nucleosome assembly in the sperm genome. Hira mutant oocytes are incapable of developing parthenogenetically, indicative of a role for Hira in the female genome. Both parental genomes show highly reduced levels of DNA replication and transcription in the mutants. It has long been thought that transcription is not required for zygote development. Surprisingly, we found that Hira/H3.3-dependent transcription of ribosomal RNA is required for first cleavage. Our results demonstrate that Hira-mediated H3.3 incorporation is essential for parental genome reprogramming and reveal an unexpected role for rRNA transcription in the mouse zygote.
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Affiliation(s)
- Chih-Jen Lin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Fong Ming Koh
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Priscilla Wong
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Marco Conti
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA.
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Chen J, Torcia S, Xie F, Lin CJ, Cakmak H, Franciosi F, Horner K, Onodera C, Song JS, Cedars MI, Ramalho-Santos M, Conti M. Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes. Nat Cell Biol 2013; 15:1415-23. [PMID: 24270888 PMCID: PMC4066669 DOI: 10.1038/ncb2873] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 10/04/2013] [Indexed: 12/15/2022]
Abstract
Germ cells divide and differentiate in a unique local microenvironment under the control of somatic cells. Signals released in this niche instruct oocyte reentry into the meiotic cell cycle. Once initiated, the progression through meiosis and the associated programme of maternal messenger RNA translation are thought to be cell autonomous. Here we show that translation of a subset of maternal mRNAs critical for embryo development is under the control of somatic cell inputs. Translation of specific maternal transcripts increases in oocytes cultured in association with somatic cells and is sensitive to EGF-like growth factors that act only on the somatic compartment. In mice deficient in amphiregulin, decreased fecundity and oocyte developmental competence is associated with defective translation of a subset of maternal mRNAs. These somatic cell signals that affect translation require activation of the PI(3)K-AKT-mTOR pathway. Thus, mRNA translation depends on somatic cell cues that are essential to reprogramme the oocyte for embryo development.
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Affiliation(s)
- Jing Chen
- 1] Center for Reproductive Sciences, University of California, San Francisco, California 94143, USA [2] Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California 94143, USA [3] Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, California 94143, USA
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Lin CJ, Conti M, Ramalho-Santos M. Histone variant H3.3 maintains a decondensed chromatin state essential for mouse preimplantation development. Development 2013; 140:3624-34. [PMID: 23903189 DOI: 10.1242/dev.095513] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Histone variants can replace canonical histones in the nucleosome and modify chromatin structure and gene expression. The histone variant H3.3 preferentially associates with active chromatin and has been implicated in the regulation of a diverse range of developmental processes. However, the mechanisms by which H3.3 may regulate gene activity are unclear and gene duplication has hampered an analysis of H3.3 function in mouse. Here, we report that the specific knockdown of H3.3 in fertilized mouse zygotes leads to developmental arrest at the morula stage. This phenotype can be rescued by exogenous H3.3 but not by canonical H3.1 mRNA. Loss of H3.3 leads to over-condensation and mis-segregation of chromosomes as early as the two-cell stage, with corresponding high levels of aneuploidy, but does not appear to affect zygotic gene activation at the two-cell stage or lineage gene transcription at the morula stage. H3.3-deficient embryos have significantly reduced levels of markers of open chromatin, such as H3K36me2 and H4K16Ac. Importantly, a mutation in H3.3K36 that disrupts H3K36 methylation (H3.3K36R) does not rescue the H3.3 knockdown (KD) phenotype. In addition, H3.3 KD embryos have increased incorporation of linker H1. Knockdown of Mof (Kat8), an acetyltransferase specific for H4K16, similarly leads to excessive H1 incorporation. Remarkably, pan-H1 RNA interference (RNAi) partially rescues the chromosome condensation of H3.3 KD embryos and allows development to the blastocyst stage. These results reveal that H3.3 mediates a balance between open and condensed chromatin that is crucial for the fidelity of chromosome segregation during early mouse development.
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Affiliation(s)
- Chih-Jen Lin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Obstetrics and Gynecology and Center for Reproductive Sciences, University of California San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
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Blaschke K, Ebata KT, Karimi MM, Zepeda-Martínez JA, Goyal P, Mahapatra S, Tam A, Laird DJ, Hirst M, Rao A, Lorincz MC, Ramalho-Santos M. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature 2013; 500:222-6. [PMID: 23812591 PMCID: PMC3893718 DOI: 10.1038/nature12362] [Citation(s) in RCA: 620] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 06/10/2013] [Indexed: 01/20/2023]
Abstract
DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germ line, and may be mediated by Tet (ten eleven translocation) enzymes, which convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Tet enzymes have been studied extensively in mouse embryonic stem (ES) cells, which are generally cultured in the absence of vitamin C, a potential cofactor for Fe(II) 2-oxoglutarate dioxygenase enzymes such as Tet enzymes. Here we report that addition of vitamin C to mouse ES cells promotes Tet activity, leading to a rapid and global increase in 5hmC. This is followed by DNA demethylation of many gene promoters and upregulation of demethylated germline genes. Tet1 binding is enriched near the transcription start site of genes affected by vitamin C treatment. Importantly, vitamin C, but not other antioxidants, enhances the activity of recombinant Tet1 in a biochemical assay, and the vitamin-C-induced changes in 5hmC and 5mC are entirely suppressed in Tet1 and Tet2 double knockout ES cells. Vitamin C has a stronger effect on regions that gain methylation in cultured ES cells compared to blastocysts, and in vivo are methylated only after implantation. In contrast, imprinted regions and intracisternal A particle retroelements, which are resistant to demethylation in the early embryo, are resistant to vitamin-C-induced DNA demethylation. Collectively, the results of this study establish vitamin C as a direct regulator of Tet activity and DNA methylation fidelity in ES cells.
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Affiliation(s)
- Kathryn Blaschke
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Obstetrics and Gynecology and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California 94143, USA
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Sachs M, Onodera C, Blaschke K, Ebata KT, Song JS, Ramalho-Santos M. Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo. Cell Rep 2013; 3:1777-84. [PMID: 23727241 DOI: 10.1016/j.celrep.2013.04.032] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 03/02/2013] [Accepted: 04/29/2013] [Indexed: 11/29/2022] Open
Abstract
Developmental regulatory genes have both activating (H3K4me3) and repressive (H3K27me3) histone modifications in embryonic stem cells (ESCs). This bivalent configuration is thought to maintain lineage commitment programs in a poised state. However, establishing physiological relevance has been complicated by the high number of cells required for chromatin immunoprecipitation (ChIP). We developed a low-cell-number chromatin immunoprecipitation (low-cell ChIP) protocol to investigate the chromatin of mouse primordial germ cells (PGCs). Genome-wide analysis of embryonic day 11.5 (E11.5) PGCs revealed H3K4me3/H3K27me3 bivalent domains highly enriched at developmental regulatory genes in a manner remarkably similar to ESCs. Developmental regulators remain bivalent and transcriptionally silent through the initiation of sexual differentiation at E13.5. We also identified >2,500 "orphan" bivalent domains that are distal to known genes and expressed in a tissue-specific manner but silent in PGCs. Our results demonstrate the existence of bivalent domains in the germline and raise the possibility that the somatic program is continuously maintained as bivalent, potentially imparting transgenerational epigenetic inheritance.
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Affiliation(s)
- Michael Sachs
- Biomedical Sciences Graduate Program, 35 Medical Center Way, University of California, San Francisco, CA 94143, USA
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Sakaki-Yumoto M, Liu J, Ramalho-Santos M, Yoshida N, Derynck R. Smad2 is essential for maintenance of the human and mouse primed pluripotent stem cell state. J Biol Chem 2013; 288:18546-60. [PMID: 23649632 DOI: 10.1074/jbc.m112.446591] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Human embryonic stem cells and mouse epiblast stem cells represent a primed pluripotent stem cell state that requires TGF-β/activin signaling. TGF-β and/or activin are commonly thought to regulate transcription through both Smad2 and Smad3. However, the different contributions of these two Smads to primed pluripotency and the downstream events that they may regulate remain poorly understood. We addressed the individual roles of Smad2 and Smad3 in the maintenance of primed pluripotency. We found that Smad2, but not Smad3, is required to maintain the undifferentiated pluripotent state. We defined a Smad2 regulatory circuit in human embryonic stem cells and mouse epiblast stem cells, in which Smad2 acts through binding to regulatory promoter sequences to activate Nanog expression while in parallel repressing autocrine bone morphogenetic protein signaling. Increased autocrine bone morphogenetic protein signaling caused by Smad2 down-regulation leads to cell differentiation toward the trophectoderm, mesoderm, and germ cell lineages. Additionally, induction of Cdx2 expression, as a result of decreased Smad2 expression, leads to repression of Oct4 expression, which, together with the decreased Nanog expression, accelerates the loss of pluripotency. These findings reveal that Smad2 is a unique integrator of transcription and signaling events and is essential for the maintenance of the mouse and human primed pluripotent stem cell state.
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Affiliation(s)
- Masayo Sakaki-Yumoto
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Program in Cell Biology, University of California, San Francisco, California 94143, USA
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Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF. Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet 2012; 8:e1002576. [PMID: 22438827 PMCID: PMC3305387 DOI: 10.1371/journal.pgen.1002576] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 01/18/2012] [Indexed: 12/25/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) trimethylates lysine 27 of histone H3 (H3K27me3) to regulate gene expression during diverse biological transitions in development, embryonic stem cell (ESC) differentiation, and cancer. Here, we show that Polycomb-like 3 (Pcl3) is a component of PRC2 that promotes ESC self-renewal. Using mass spectrometry, we identified Pcl3 as a Suz12 binding partner and confirmed Pcl3 interactions with core PRC2 components by co-immunoprecipitation. Knockdown of Pcl3 in ESCs increases spontaneous differentiation, yet does not affect early differentiation decisions as assessed in teratomas and embryoid bodies, indicating that Pcl3 has a specific role in regulating ESC self-renewal. Consistent with Pcl3 promoting PRC2 function, decreasing Pcl3 levels reduces H3K27me3 levels while overexpressing Pcl3 increases H3K27me3 levels. Furthermore, chromatin immunoprecipitation and sequencing (ChIP-seq) reveal that Pcl3 co-localizes with PRC2 core component, Suz12, and depletion of Pcl3 decreases Suz12 binding at over 60% of PRC2 targets. Mutation of conserved residues within the Pcl3 Tudor domain, a domain implicated in recognizing methylated histones, compromises H3K27me3 formation, suggesting that the Tudor domain of Pcl3 is essential for function. We also show that Pcl3 and its paralog, Pcl2, exist in different PRC2 complexes but bind many of the same PRC2 targets, particularly CpG islands regulated by Pcl3. Thus, Pcl3 is a component of PRC2 critical for ESC self-renewal, histone methylation, and recruitment of PRC2 to a subset of its genomic sites.
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Affiliation(s)
- Julie Hunkapiller
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Yin Shen
- Ludwig Institute for Cancer Research, School of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Aaron Diaz
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - David McCleary
- Ludwig Institute for Cancer Research, School of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Miguel Ramalho-Santos
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Bing Ren
- Ludwig Institute for Cancer Research, School of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Jun S. Song
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Biostatistics and Epidemiology, Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (JSS); (JFR)
| | - Jeremy F. Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (JSS); (JFR)
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Qin H, Blaschke K, Wei G, Ohi Y, Blouin L, Qi Z, Yu J, Yeh RF, Hebrok M, Ramalho-Santos M. Transcriptional analysis of pluripotency reveals the Hippo pathway as a barrier to reprogramming. Hum Mol Genet 2012; 21:2054-67. [PMID: 22286172 DOI: 10.1093/hmg/dds023] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pluripotent stem cells are derived from culture of early embryos or the germline and can be induced by reprogramming of somatic cells. Barriers to reprogramming that stabilize the differentiated state and have tumor suppression functions are expected to exist. However, we have a limited understanding of what such barriers might be. To find novel barriers to reprogramming to pluripotency, we compared the transcriptional profiles of the mouse germline with pluripotent and somatic cells, in vivo and in vitro. There is a remarkable global expression of the transcriptional program for pluripotency in primordial germ cells (PGCs). We identify parallels between PGC reprogramming to pluripotency and human germ cell tumorigenesis, including the loss of LATS2, a tumor suppressor kinase of the Hippo pathway. We show that knockdown of LATS2 increases the efficiency of induction of pluripotency in human cells. LATS2 RNAi, unlike p53 RNAi, specifically enhances the generation of fully reprogrammed iPS cells without accelerating cell proliferation. We further show that LATS2 represses reprogramming in human cells by post-transcriptionally antagonizing TAZ but not YAP, two downstream effectors of the Hippo pathway. These results reveal transcriptional parallels between germ cell transformation and the generation of iPS cells and indicate that the Hippo pathway constitutes a barrier to cellular reprogramming.
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Affiliation(s)
- Han Qin
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Diabetes Center, South San Francisco, CA, USA
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Gaspar-Maia A, Alajem A, Meshorer E, Ramalho-Santos M. Erratum: Open chromatin in pluripotency and reprogramming. Nat Rev Mol Cell Biol 2011. [DOI: 10.1038/nrm3077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Koh FM, Sachs M, Guzman-Ayala M, Ramalho-Santos M. Parallel gateways to pluripotency: open chromatin in stem cells and development. Curr Opin Genet Dev 2010; 20:492-9. [PMID: 20598875 DOI: 10.1016/j.gde.2010.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 05/20/2010] [Accepted: 06/02/2010] [Indexed: 12/23/2022]
Abstract
Open chromatin is a hallmark of pluripotent stem cells, but the underlying molecular mechanisms are only beginning to be unraveled. In this review we highlight recent studies that employ embryonic stem cells and induced pluripotent stem cells to investigate the regulation of open chromatin and its role in the maintenance and acquisition of pluripotency in vitro. We suggest that findings from in vitro studies using pluripotent stem cells are predictive of in vivo processes of epigenetic regulation of pluripotency, specifically in the development of the zygote and primordial germ cells. The combination of in vitro and in vivo approaches is expected to provide a comprehensive understanding of the epigenetic regulation of pluripotency and reprograming.
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Affiliation(s)
- Fong Ming Koh
- Departments of Ob/Gyn and Pathology, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143-0525, USA
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Abstract
The discovery that adult somatic cells can be induced to become pluripotent by overexpression of a few key transcription factors provides an exciting new window into the basic biology of pluripotency and differentiation.
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Affiliation(s)
- Miguel Ramalho-Santos
- Department of Ob/Gyn, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143-0525, USA.
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Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H. CompMoby: comparative MobyDick for detection of cis-regulatory motifs. BMC Bioinformatics 2008; 9:455. [PMID: 18950538 PMCID: PMC2605473 DOI: 10.1186/1471-2105-9-455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 10/27/2008] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The regulation of gene expression is complex and occurs at many levels, including transcriptional and post-transcriptional, in metazoans. Transcriptional regulation is mainly determined by sequence elements within the promoter regions of genes while sequence elements within the 3' untranslated regions of mRNAs play important roles in post-transcriptional regulation such as mRNA stability and translation efficiency. Identifying cis-regulatory elements, or motifs, in multicellular eukaryotes is more difficult compared to unicellular eukaryotes due to the larger intergenic sequence space and the increased complexity in regulation. Experimental techniques for discovering functional elements are often time consuming and not easily applied on a genome level. Consequently, computational methods are advantageous for genome-wide cis-regulatory motif detection. To decrease the search space in metazoans, many algorithms use cross-species alignment, although studies have demonstrated that a large portion of the binding sites for the same trans-acting factor do not reside in alignable regions. Therefore, a computational algorithm should account for both conserved and nonconserved cis-regulatory elements in metazoans. RESULTS We present CompMoby (Comparative MobyDick), software developed to identify cis-regulatory binding sites at both the transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factors. The CompMoby algorithm was previously shown to identify cis-regulatory binding sites in upstream regions of genes co-regulated in embryonic stem cells. In this paper, we extend the software to identify putative cis-regulatory motifs in 3' UTR sequences and verify our results using experimentally validated data sets in mouse and human. We also detail the implementation of CompMoby into a user-friendly tool that includes a web interface to a streamlined analysis. Our software allows detection of motifs in the following three categories: one, those that are alignable and conserved; two, those that are conserved but not alignable; three, those that are species specific. One of the output files from CompMoby gives the user the option to decide what category of cis-regulatory element to experimentally pursue based on their biological problem. Using experimentally validated biological datasets, we demonstrate that CompMoby is successful in detecting cis-regulatory target sites of known and novel trans-acting factors at the transcriptional and post-transcriptional levels. CONCLUSION CompMoby is a powerful software tool for systematic de novo discovery of evolutionarily conserved and nonconserved cis-regulatory sequences involved in transcriptional or post-transcriptional regulation in metazoans. This software is freely available to users at http://genome.ucsf.edu/compmoby/.
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Affiliation(s)
- Christina Chaivorapol
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biomedical Research, Graduate Program in Biological and Medical Informatics, University of California, San Francisco, CA 94143-2540, USA.
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Wong CC, Gaspar-Maia A, Ramalho-Santos M, Reijo Pera RA. High-efficiency stem cell fusion-mediated assay reveals Sall4 as an enhancer of reprogramming. PLoS One 2008; 3:e1955. [PMID: 18414659 PMCID: PMC2278370 DOI: 10.1371/journal.pone.0001955] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 03/02/2008] [Indexed: 01/23/2023] Open
Abstract
Several methods allow reprogramming of differentiated somatic cells to embryonic stem cell-like cells. However, the process of reprogramming remains inefficient and the underlying molecular mechanisms are poorly understood. Here, we report the optimization of somatic cell fusion with embryonic stem cells in order to provide an efficient, quantitative assay to screen for factors that facilitate reprogramming. Following optimization, we achieved a reprogramming efficiency 15–590 fold higher than previous protocols. This allowed observation of cellular events during the reprogramming process. Moreover, we demonstrate that overexpression of the Spalt transcription factor, Sall4, which was previously identified as a regulator of embryonic stem cell pluripotency and early mouse development, can enhance reprogramming. The reprogramming activity of Sall4 is independent of an N-terminal domain implicated in recruiting the nucleosome remodeling and deacetylase corepressor complex, a global transcriptional repressor. These results indicate that improvements in reprogramming assays, including fusion assays, may allow the systematic identification and molecular characterization of enhancers of somatic cell reprogramming.
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Affiliation(s)
- Connie C. Wong
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Alexandre Gaspar-Maia
- Institute for Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
- Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- Doctoral Program in Biomedicine and Experimental Biology, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Miguel Ramalho-Santos
- Institute for Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
- Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail: (MR); (RR)
| | - Renee A. Reijo Pera
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail: (MR); (RR)
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Grskovic M, Chaivorapol C, Gaspar-Maia A, Li H, Ramalho-Santos M. Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells. PLoS Genet 2007; 3:e145. [PMID: 17784790 PMCID: PMC1959362 DOI: 10.1371/journal.pgen.0030145] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 07/10/2007] [Indexed: 01/06/2023] Open
Abstract
Understanding the transcriptional regulation of pluripotent cells is of fundamental interest and will greatly inform efforts aimed at directing differentiation of embryonic stem (ES) cells or reprogramming somatic cells. We first analyzed the transcriptional profiles of mouse ES cells and primordial germ cells and identified genes upregulated in pluripotent cells both in vitro and in vivo. These genes are enriched for roles in transcription, chromatin remodeling, cell cycle, and DNA repair. We developed a novel computational algorithm, CompMoby, which combines analyses of sequences both aligned and non-aligned between different genomes with a probabilistic segmentation model to systematically predict short DNA motifs that regulate gene expression. CompMoby was used to identify conserved overrepresented motifs in genes upregulated in pluripotent cells. We show that the motifs are preferentially active in undifferentiated mouse ES and embryonic germ cells in a sequence-specific manner, and that they can act as enhancers in the context of an endogenous promoter. Importantly, the activity of the motifs is conserved in human ES cells. We further show that the transcription factor NF-Y specifically binds to one of the motifs, is differentially expressed during ES cell differentiation, and is required for ES cell proliferation. This study provides novel insights into the transcriptional regulatory networks of pluripotent cells. Our results suggest that this systematic approach can be broadly applied to understanding transcriptional networks in mammalian species. Embryonic stem cells have two remarkable properties: they can proliferate very rapidly, and they can give rise to all of the body's cell types. Understanding how gene activity is regulated in embryonic stem cells will be an important step towards therapeutic applications. The activity of genes is regulated by proteins called transcription factors, which bind to stretches of DNA sequences that act as on or off switches. We identified genes that are active in mouse embryonic stem cells but not in differentiated cells. We reasoned that if these genes have similar patterns of activity, they may be regulated by the same transcription factors. We therefore developed a computational approach that takes information on gene activity and predicts DNA sequences that may act as switches. Using this approach, we discovered new DNA switches that regulate gene activity in mouse and human embryonic stem cells. Furthermore, we identified a transcription factor that binds to one of these DNA switches and is important for the rapid proliferation of embryonic stem cells. Our approach sheds light on the genetic regulation of embryonic stem cells and will be broadly applicable to questions of how gene activity is regulated in other cell types of interest.
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Affiliation(s)
- Marica Grskovic
- Institute for Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
- Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
| | - Christina Chaivorapol
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Graduate Program in Biological and Medical Informatics; University of California San Francisco, San Francisco, California, United States of America
| | - Alexandre Gaspar-Maia
- Institute for Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
- Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- Doctoral Program in Biomedicine and Experimental Biology, Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Graduate Program in Biological and Medical Informatics; University of California San Francisco, San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail: (HL); (MRS)
| | - Miguel Ramalho-Santos
- Institute for Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
- Diabetes Center, University of California San Francisco, San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail: (HL); (MRS)
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Heidersbach A, Gaspar-Maia A, McManus MT, Ramalho-Santos M. RNA interference in embryonic stem cells and the prospects for future therapies. Gene Ther 2006; 13:478-86. [PMID: 16520820 DOI: 10.1038/sj.gt.3302723] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In 1998, two distinct and exciting scientific fields emerged which have profoundly shaped the current direction of biomedical research. The discovery of RNA interference (RNAi) and the derivation of human embryonic stem (ES) cells have yielded exciting new possibilities for researchers and clinicians alike. While fundamentally different, aspects from these two fields may be combined to yield extraordinary scientific and medical benefits. Here, we review the prospects of combining RNAi and ES cell manipulation for both basic research and future therapies, as well as current limitations and obstacles that need to be overcome.
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Affiliation(s)
- A Heidersbach
- Diabetes Center, University of California, San Francisco, CA 94143-0525, USA
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Abstract
Stem cells have the capacity both to self-renew and to give rise to differentiated progeny, and are vital to the organization of multicellular organisms. Stem cells raise a number of fundamental questions regarding lineage restriction and cellular differentiation, and they hold enormous promise for cell-based therapies. Here I propose a theoretical framework for stem cell biology based on the concepts of autopoiesis (self-production) and complementarity. I argue that stem cells are pivotal in the self-production of the organism and that we need complementary approaches to understand their probabilistic behavior. I discuss how this framework generates testable hypotheses regarding stem-cell functions.
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Affiliation(s)
- Miguel Ramalho-Santos
- Program in Developmental and Stem Cell Biology, University of California, San Francisco, San Francisco CA 94143-0540, USA.
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Abstract
The transcriptional profiles of mouse embryonic, neural, and hematopoietic stem cells were compared to define a genetic program for stem cells. A total of 216 genes are enriched in all three types of stem cells, and several of these genes are clustered in the genome. When compared to differentiated cell types, stem cells express a significantly higher number of genes (represented by expressed sequence tags) whose functions are unknown. Embryonic and neural stem cells have many similarities at the transcriptional level. These results provide a foundation for a more detailed understanding of stem cell biology.
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Affiliation(s)
- Miguel Ramalho-Santos
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute (HHMI), Harvard University, Cambridge, MA 02138, USA
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Zhang XM, Ramalho-Santos M, McMahon AP. Smoothened mutants reveal redundant roles for Shh and Ihh signaling including regulation of L/R symmetry by the mouse node. Cell 2001; 106:781-92. [PMID: 11517919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Genetic analyses in Drosophila have demonstrated that the multipass membrane protein Smoothened (Smo) is essential for all Hedgehog signaling. We show that Smo acts epistatic to Ptc1 to mediate Shh and Ihh signaling in the early mouse embryo. Smo and Shh/Ihh compound mutants have identical phenotypes: embryos fail to turn, arresting at somite stages with a small, linear heart tube, an open gut and cyclopia. The absence of visible left/right (L/R) asymmetry led us to examine the pathways controlling L/R situs. We present evidence consistent with a model in which Hedgehog signaling within the node is required for activation of Gdf1, and induction of left-side determinants. Further, we demonstrate an absolute requirement for Hedgehog signaling in sclerotomal development and a role in cardiac morphogenesis.
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MESH Headings
- Animals
- Body Patterning
- DNA-Binding Proteins
- Drosophila Proteins
- Embryo, Mammalian/embryology
- Embryo, Mammalian/metabolism
- Embryonic Induction
- Epistasis, Genetic
- Gene Expression Regulation, Developmental
- Growth Differentiation Factor 1
- Growth Substances/genetics
- Heart/embryology
- Heart/physiology
- Hedgehog Proteins
- Homeobox Protein Nkx-2.5
- Homeodomain Proteins/genetics
- In Situ Hybridization
- Intercellular Signaling Peptides and Proteins
- Membrane Proteins/genetics
- Mice
- Models, Biological
- Muscle Proteins/genetics
- Mutation/genetics
- Myogenic Regulatory Factor 5
- Nerve Tissue Proteins/genetics
- Patched Receptors
- Patched-1 Receptor
- Proteins/genetics
- Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Receptors, G-Protein-Coupled
- Signal Transduction
- Smoothened Receptor
- Somites/metabolism
- Trans-Activators
- Transcription Factors/genetics
- Xenopus Proteins
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Affiliation(s)
- X M Zhang
- Department of Molecular and Cellular Biology, The Biolabs, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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Zhang XM, Ramalho-Santos M, McMahon AP. Smoothened mutants reveal redundant roles for Shh and Ihh signaling including regulation of L/R asymmetry by the mouse node. Cell 2001; 105:781-92. [PMID: 11440720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Genetic analyses in Drosophila have demonstrated that the multipass membrane protein Smoothened (Smo) is essential for all Hedgehog signaling. We show that Smo acts epistatic to Ptc1 to mediate Shh and Ihh signaling in the early mouse embryo. Smo and Shh/Ihh compound mutants have identical phenotypes: embryos fail to turn, arresting at somite stages with a small, linear heart tube, an open gut and cyclopia. The absence of visible left/right (L/R) asymmetry led us to examine the pathways controlling L/R situs. We present evidence consistent with a model in which Hedgehog signaling within the node is required for activation of Gdf1, and induction of left-side determinants. Further, we demonstrate an absolute requirement for Hedgehog signaling in sclerotomal development and a role in cardiac morphogenesis.[Dedicated to Rosa Beddington, a pioneer in mammalian embryology].
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MESH Headings
- Animals
- Body Patterning
- DNA-Binding Proteins
- Drosophila Proteins
- Embryo, Mammalian/embryology
- Embryo, Mammalian/metabolism
- Embryonic Induction
- Epistasis, Genetic
- Gene Expression Regulation, Developmental
- Growth Differentiation Factor 1
- Growth Substances/genetics
- Heart/embryology
- Heart/physiology
- Hedgehog Proteins
- Homeobox Protein Nkx-2.5
- Homeodomain Proteins/genetics
- In Situ Hybridization
- Intercellular Signaling Peptides and Proteins
- Membrane Proteins/genetics
- Mice
- Models, Biological
- Muscle Proteins/genetics
- Mutation/genetics
- Myogenic Regulatory Factor 5
- Nerve Tissue Proteins/genetics
- Patched Receptors
- Patched-1 Receptor
- Proteins/genetics
- Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Receptors, G-Protein-Coupled
- Signal Transduction
- Smoothened Receptor
- Somites/metabolism
- Trans-Activators
- Transcription Factors/genetics
- Xenopus Proteins
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Affiliation(s)
- X M Zhang
- Department of Molecular and Cellular Biology, The Biolabs, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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Zhang XM, Ramalho-Santos M, McMahon AP. Smoothened Mutants Reveal Redundant Roles for Shh and Ihh Signaling Including Regulation of L/R Asymmetry by the Mouse Node. Cell 2001. [DOI: 10.1016/s0092-8674(01)00385-3] [Citation(s) in RCA: 472] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
The gastrointestinal tract develops from the embryonic gut, which is composed of an endodermally derived epithelium surrounded by cells of mesodermal origin. Cell signaling between these two tissue layers appears to play a critical role in coordinating patterning and organogenesis of the gut and its derivatives. We have assessed the function of Sonic hedgehog and Indian hedgehog genes, which encode members of the Hedgehog family of cell signals. Both are expressed in gut endoderm, whereas target genes are expressed in discrete layers in the mesenchyme. It was unclear whether functional redundancy between the two genes would preclude a genetic analysis of the roles of Hedgehog signaling in the mouse gut. We show here that the mouse gut has both common and separate requirements for Sonic hedgehog and Indian hedgehog. Both Sonic hedgehog and Indian hedgehog mutant mice show reduced smooth muscle, gut malrotation and annular pancreas. Sonic hedgehog mutants display intestinal transformation of the stomach, duodenal stenosis (obstruction), abnormal innervation of the gut and imperforate anus. Indian hedgehog mutants show reduced epithelial stem cell proliferation and differentiation, together with features typical of Hirschsprung's disease (aganglionic colon). These results show that Hedgehog signals are essential for organogenesis of the mammalian gastrointestinal tract and suggest that mutations in members of this signaling pathway may be involved in human gastrointestinal malformations.
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Affiliation(s)
- M Ramalho-Santos
- Department of Molecular and Cellular Biology, and Howard Hughes Medical Institute, Harvard University, Divinity Avenue, Cambridge, Massachusetts 02138, USA
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Haggarty SJ, Ramalho-Santos M. Will cell alliance breed bureaucracy and leave contributors out? Nature 2000; 403:591. [PMID: 10688171 DOI: 10.1038/35001228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Faro C, Ramalho-Santos M, Vieira M, Mendes A, Simões I, Andrade R, Veríssimo P, Lin X, Tang J, Pires E. Cloning and characterization of cDNA encoding cardosin A, an RGD-containing plant aspartic proteinase. J Biol Chem 1999; 274:28724-9. [PMID: 10497243 DOI: 10.1074/jbc.274.40.28724] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cardosin A is an abundant aspartic proteinase from pistils of Cynara cardunculus L. whose milk-clotting activity has been exploited for the manufacture of cheese. Here we report the cloning and characterization of cardosin A cDNA. The deduced amino acid sequence contains the conserved features of plant aspartic proteinases, including the plant-specific insertion (PSI), and revealed the presence of an Arg-Gly-Asp (RGD) motif, which is known to function in cell surface receptor binding by extracellular proteins. Cardosin A mRNA was detected predominantly in young flower buds but not in mature or senescent pistils, suggesting that its expression is likely to be developmentally regulated. Procardosin A, the single chain precursor, was found associated with microsomal membranes of flower buds, whereas the active two-chain enzyme generated upon removal of PSI is soluble. This result implies a role for PSI in promoting the association of plant aspartic proteinase precursors to cell membranes. To get further insights about cardosin A, the functional relevance of the RGD motif was also investigated. A 100-kDa protein that interacts specifically with the RGD sequence was isolated from octyl glucoside pollen extracts by affinity chromatography on cardosin A-Sepharose. This result suggests that the 100-kDa protein is a cardosin A receptor and indicates that the interaction between these two proteins is apparently mediated through RGD recognition. It is possible therefore that cardosin A may have a role in adhesion-mediated proteolytic mechanisms involved in pollen recognition and growth.
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Affiliation(s)
- C Faro
- Departamento de Bioquímica, Faculdade de Ciências e Tecnologia, Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3000 Coimbra, Portugal
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Ramalho-Santos M, Veríssimo P, Cortes L, Samyn B, Van Beeumen J, Pires E, Faro C. Identification and proteolytic processing of procardosin A. Eur J Biochem 1998; 255:133-8. [PMID: 9692911 DOI: 10.1046/j.1432-1327.1998.2550133.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Plant aspartic proteinases contain a plant-specific insert (PSI) of about 100 amino acids of unknown function with no similarity with the other aspartic proteinases but with significant similarity with saposins, animal sphingolipid activator proteins. PSI has remained elusive at the protein level, suggesting that it may be removed during processing. To understand the molecular relevance of PSI, the proteolytic processing of cardosin A, the major aspartic proteinase from the flowers of cardoon (Cynara cardunculus L.) was studied. Procardosin A, a 64-kDa cardosin A precursor containing PSI and the prosegment was identified by immunoblotting using monospecific antibodies against PSI and the prosegment. Procardosin A undergoes proteolytic processing as the flower matures. PSI was found to be removed before the prosegment, indicating that during processing the enzyme acquires a structure typical of mammalian or microbial aspartic proteinase proforms. In vitro studies showed that processing of PSI occurs at pH 3.0 and is inhibited by pepstatin A and at pH 7.0. Sequence analysis allowed the identification of the cleavage sites, revealing that PSI is removed entirely, probably by an aspartic proteinase. Cleavage of the PSI scissile bonds requires, however, a conformation specific to the precursor since isolated cardosins and pistil extracts were unable to hydrolyse synthetic peptides corresponding to the cleavage sites. In view of these results, a model for the proteolytic processing of cardosin A is proposed and the molecular and physiological relevance of PSI in plant aspartic proteinase is discussed.
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Affiliation(s)
- M Ramalho-Santos
- Departamento de Bioquímica and the Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Portugal
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Faro C, Ramalho-Santos M, Veríssimo P, Pissarra J, Frazão C, Costa J, Lin XL, Tang J, Pires E. Structural and functional aspects of cardosins. Adv Exp Med Biol 1998; 436:423-33. [PMID: 9580379 DOI: 10.1007/978-1-4615-5373-1_58] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- C Faro
- Departamento Bioquímica, Universidade de Coimbra, Portugal
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Ramalho-Santos M, Pissarra J, Pires E, Faro C. Cardosinogen A. The precursor form of the major aspartic proteinase from cardoon. Adv Exp Med Biol 1998; 436:253-8. [PMID: 9561227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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