1
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Forouzanfar F, Plassard D, Furst A, Moreno D, Oliveira KA, Reina-San-Martin B, Tora L, Molina N, Mendoza M. Gene-specific RNA homeostasis revealed by perturbation of coactivator complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.577960. [PMID: 38352321 PMCID: PMC10862879 DOI: 10.1101/2024.01.30.577960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Transcript buffering entails the reciprocal modulation of mRNA synthesis and degradation rates to maintain stable RNA levels under varying cellular conditions. Current research supports a global, non-sequence-specific connection between mRNA synthesis and degradation, but the underlying mechanisms are still unclear. In this study, we investigated changes in RNA metabolism following acute depletion of TIP60/KAT5, the acetyltransferase subunit of the NuA4 transcriptional coactivator complex, in mouse embryonic stem cells. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling, we demonstrate that TIP60 predominantly enhances transcription of numerous genes, while a smaller set of genes undergoes TIP60-dependent transcriptional repression. Surprisingly, transcription changes caused by TIP60 depletion were offset by corresponding changes in RNA nuclear export and cytoplasmic stability, indicating gene-specific buffering mechanisms. Similarly, disruption of the unrelated ATAC coactivator complex also resulted in gene-specific transcript buffering. These findings reveal that transcript buffering functions at a gene-specific level and suggest that cells dynamically adjust RNA splicing, export, and degradation in response to individual RNA synthesis alterations, thereby sustaining cellular homeostasis.
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2
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Chialastri A, Sarkar S, Schauer EE, Lamba S, Dey SS. Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity. Nat Struct Mol Biol 2024:10.1038/s41594-024-01291-w. [PMID: 38671229 DOI: 10.1038/s41594-024-01291-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
Inheritance of 5-methylcytosine from one cell generation to the next by DNA methyltransferase 1 (DNMT1) plays a key role in regulating cellular identity. While recent work has shown that the activity of DNMT1 is imprecise, it remains unclear how the fidelity of DNMT1 is tuned in different genomic and cell state contexts. Here we describe Dyad-seq, a method to quantify the genome-wide methylation status of cytosines at the resolution of individual CpG dinucleotides to find that the fidelity of DNMT1-mediated maintenance methylation is related to the local density of DNA methylation and the landscape of histone modifications. To gain deeper insights into methylation/demethylation turnover dynamics, we first extended Dyad-seq to quantify all combinations of 5-methylcytosine and 5-hydroxymethylcytosine at individual CpG dyads. Next, to understand how cell state transitions impact maintenance methylation, we scaled the method down to jointly profile genome-wide methylation levels, maintenance methylation fidelity and the transcriptome from single cells (scDyad&T-seq). Using scDyad&T-seq, we demonstrate that, while distinct cell states can substantially impact the activity of the maintenance methylation machinery, locally there exists an intrinsic relationship between DNA methylation density, histone modifications and DNMT1-mediated maintenance methylation fidelity that is independent of cell state.
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Affiliation(s)
- Alex Chialastri
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Saumya Sarkar
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Elizabeth E Schauer
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Shyl Lamba
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA, USA
| | - Siddharth S Dey
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA.
- Department of Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA.
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
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3
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Brahma S, Henikoff S. The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes. Nat Genet 2024; 56:100-111. [PMID: 38049663 PMCID: PMC10786724 DOI: 10.1038/s41588-023-01603-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023]
Abstract
Chromatin accessibility is a hallmark of active transcription and entails ATP-dependent nucleosome remodeling, which is carried out by complexes such as Brahma-associated factor (BAF). However, the mechanistic links between transcription, nucleosome remodeling and chromatin accessibility are unclear. Here, we used a chemical-genetic approach coupled with time-resolved chromatin profiling to dissect the interplay between RNA Polymerase II (RNAPII), BAF and DNA-sequence-specific transcription factors in mouse embryonic stem cells. We show that BAF dynamically unwraps and evicts nucleosomes at accessible chromatin regions, while RNAPII promoter-proximal pausing stabilizes BAF chromatin occupancy and enhances ATP-dependent nucleosome eviction by BAF. We find that although RNAPII and BAF dynamically probe both transcriptionally active and Polycomb-repressed genomic regions, pluripotency transcription factor chromatin binding confers locus specificity for productive chromatin remodeling and nucleosome eviction by BAF. Our study suggests a paradigm for how functional synergy between dynamically acting chromatin factors regulates locus-specific nucleosome organization and chromatin accessibility.
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Affiliation(s)
- Sandipan Brahma
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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4
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Sahay S, Adhikari S, Hormoz S, Chakrabarti S. An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells. BIOINFORMATICS (OXFORD, ENGLAND) 2023; 39:btad602. [PMID: 37769241 PMCID: PMC10576164 DOI: 10.1093/bioinformatics/btad602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 09/30/2023]
Abstract
MOTIVATION Detecting oscillations in time series remains a challenging problem even after decades of research. In chronobiology, rhythms (for instance in gene expression, eclosion, egg-laying, and feeding) tend to be low amplitude, display large variations amongst replicates, and often exhibit varying peak-to-peak distances (non-stationarity). Most currently available rhythm detection methods are not specifically designed to handle such datasets, and are also limited by their use of P-values in detecting oscillations. RESULTS We introduce a new method, ODeGP (Oscillation Detection using Gaussian Processes), which combines Gaussian Process regression and Bayesian inference to incorporate measurement errors, non-uniformly sampled data, and a recently developed non-stationary kernel to improve detection of oscillations. By using Bayes factors, ODeGP models both the null (non-rhythmic) and the alternative (rhythmic) hypotheses, thus providing an advantage over P-values. Using synthetic datasets, we first demonstrate that ODeGP almost always outperforms eight commonly used methods in detecting stationary as well as non-stationary symmetric oscillations. Next, by analyzing existing qPCR datasets, we demonstrate that our method is more sensitive compared to the existing methods at detecting weak and noisy oscillations. Finally, we generate new qPCR data on mouse embryonic stem cells. Surprisingly, we discover using ODeGP that increasing cell-density results in rapid generation of oscillations in the Bmal1 gene, thus highlighting our method's ability to discover unexpected and new patterns. In its current implementation, ODeGP is meant only for analyzing single or a few time-trajectories, not genome-wide datasets. AVAILABILITY AND IMPLEMENTATION ODeGP is available at https://github.com/Shaonlab/ODeGP.
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Affiliation(s)
- Shabnam Sahay
- Department of Computer Science, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, India
| | - Shishir Adhikari
- Department of Systems Biology, Harvard Medical School, Boston, MA 02215, United States
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, United States
| | - Sahand Hormoz
- Department of Systems Biology, Harvard Medical School, Boston, MA 02215, United States
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Shaon Chakrabarti
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, India
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5
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Reimann A, Kull T, Wang W, Dettinger P, Loeffler D, Schroeder T. Embryonic stem cell ERK, AKT, plus STAT3 response dynamics combinatorics are heterogeneous but NANOG state independent. Stem Cell Reports 2023:S2213-6711(23)00142-X. [PMID: 37207650 DOI: 10.1016/j.stemcr.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023] Open
Abstract
Signaling is central in cell fate regulation, and relevant information is encoded in its activity over time (i.e., dynamics). However, simultaneous dynamics quantification of several pathways in single mammalian stem cells has not yet been accomplished. Here we generate mouse embryonic stem cell (ESC) lines simultaneously expressing fluorescent reporters for ERK, AKT, and STAT3 signaling activity, which all control pluripotency. We quantify their single-cell dynamics combinations in response to different self-renewal stimuli and find striking heterogeneity for all pathways, some dependent on cell cycle but not pluripotency states, even in ESC populations currently assumed to be highly homogeneous. Pathways are mostly independently regulated, but some context-dependent correlations exist. These quantifications reveal surprising single-cell heterogeneity in the important cell fate control layer of signaling dynamics combinations and raise fundamental questions about the role of signaling in (stem) cell fate control.
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Affiliation(s)
- Andreas Reimann
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Tobias Kull
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Weijia Wang
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Philip Dettinger
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Dirk Loeffler
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
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6
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Chialastri A, Sarkar S, Schauer EE, Lamba S, Dey SS. Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.539708. [PMID: 37205524 PMCID: PMC10187321 DOI: 10.1101/2023.05.06.539708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Transmission of 5-methylcytosine (5mC) from one cell generation to the next plays a key role in regulating cellular identity in mammalian development and diseases. While recent work has shown that the activity of DNMT1, the protein responsible for the stable inheritance of 5mC from mother to daughter cells, is imprecise; it remains unclear how the fidelity of DNMT1 is tuned in different genomic and cell state contexts. Here we describe Dyad-seq, a method that combines enzymatic detection of modified cytosines with nucleobase conversion techniques to quantify the genome-wide methylation status of cytosines at the resolution of individual CpG dinucleotides. We find that the fidelity of DNMT1-mediated maintenance methylation is directly related to the local density of DNA methylation, and for genomic regions that are lowly methylated, histone modifications can dramatically alter the maintenance methylation activity. Further, to gain deeper insights into the methylation and demethylation turnover dynamics, we extended Dyad-seq to quantify all combinations of 5mC and 5-hydroxymethylcytosine (5hmC) at individual CpG dyads to show that TET proteins preferentially hydroxymethylate only one of the two 5mC sites in a symmetrically methylated CpG dyad rather than sequentially convert both 5mC to 5hmC. To understand how cell state transitions impact DNMT1-mediated maintenance methylation, we scaled the method down and combined it with the measurement of mRNA to simultaneously quantify genome-wide methylation levels, maintenance methylation fidelity and the transcriptome from the same cell (scDyad&T-seq). Applying scDyad&T-seq to mouse embryonic stem cells transitioning from serum to 2i conditions, we observe dramatic and heterogenous demethylation and the emergence of transcriptionally distinct subpopulations that are closely linked to the cell-to-cell variability in loss of DNMT1-mediated maintenance methylation activity, with regions of the genome that escape 5mC reprogramming retaining high levels of maintenance methylation fidelity. Overall, our results demonstrate that while distinct cell states can substantially impact the genome-wide activity of the DNA methylation maintenance machinery, locally there exists an intrinsic relationship between DNA methylation density, histone modifications and DNMT1-mediated maintenance methylation fidelity that is independent of cell state.
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Affiliation(s)
- Alex Chialastri
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Saumya Sarkar
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Elizabeth E. Schauer
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Shyl Lamba
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Siddharth S. Dey
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
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7
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Sahay S, Adhikari S, Hormoz S, Chakrabarti S. An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533651. [PMID: 36993318 PMCID: PMC10055182 DOI: 10.1101/2023.03.21.533651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Detecting oscillations in time series remains a challenging problem even after decades of research. In chronobiology, rhythms in time series (for instance gene expression, eclosion, egg-laying and feeding) datasets tend to be low amplitude, display large variations amongst replicates, and often exhibit varying peak-to-peak distances (non-stationarity). Most currently available rhythm detection methods are not specifically designed to handle such datasets. Here we introduce a new method, ODeGP ( O scillation De tection using G aussian P rocesses), which combines Gaussian Process (GP) regression with Bayesian inference to provide a flexible approach to the problem. Besides naturally incorporating measurement errors and non-uniformly sampled data, ODeGP uses a recently developed kernel to improve detection of non-stationary waveforms. An additional advantage is that by using Bayes factors instead of p-values, ODeGP models both the null (non-rhythmic) and the alternative (rhythmic) hypotheses. Using a variety of synthetic datasets we first demonstrate that ODeGP almost always outperforms eight commonly used methods in detecting stationary as well as non-stationary oscillations. Next, on analyzing existing qPCR datasets that exhibit low amplitude and noisy oscillations, we demonstrate that our method is more sensitive compared to the existing methods at detecting weak oscillations. Finally, we generate new qPCR time-series datasets on pluripotent mouse embryonic stem cells, which are expected to exhibit no oscillations of the core circadian clock genes. Surprisingly, we discover using ODeGP that increasing cell density can result in the rapid generation of oscillations in the Bmal1 gene, thus highlighting our method’s ability to discover unexpected patterns. In its current implementation, ODeGP (available as an R package) is meant only for analyzing single or a few time-trajectories, not genome-wide datasets.
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Affiliation(s)
- Shabnam Sahay
- Department of Computer Science, Indian Institute of Technology Bombay
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore
| | - Shishir Adhikari
- Department of Systems Biology, Harvard Medical School, Boston
- Department of Data Science, Dana-Farber Cancer Institute, Boston
| | - Sahand Hormoz
- Department of Systems Biology, Harvard Medical School, Boston
- Department of Data Science, Dana-Farber Cancer Institute, Boston
- Broad Institute of MIT and Harvard, Cambridge
| | - Shaon Chakrabarti
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore
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8
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Brahma S, Henikoff S. RNA Polymerase II, the BAF remodeler and transcription factors synergize to evict nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525083. [PMID: 36711459 PMCID: PMC9882304 DOI: 10.1101/2023.01.22.525083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chromatin accessibility is a hallmark of active transcription and requires ATP-dependent nucleosome remodeling by Brahma-Associated Factor (BAF). However, the mechanistic link between transcription, nucleosome remodeling, and chromatin accessibility is unclear. Here, we used a chemical-genetic approach to dissect the interplay between RNA Polymerase II (RNAPII), BAF, and DNA-sequence-specific transcription factors (TFs) in mouse embryonic stem cells. By time-resolved chromatin profiling with acute transcription block at distinct stages, we show that RNAPII promoter-proximal pausing stabilizes BAF chromatin occupancy and enhances nucleosome eviction by BAF. We find that RNAPII and BAF probe both transcriptionally active and Polycomb-repressed genomic regions and provide evidence that TFs capture transient site exposure due to nucleosome unwrapping by BAF to confer locus specificity for persistent chromatin remodeling. Our study reveals the mechanistic basis of cell-type-specific chromatin accessibility. We propose a new paradigm for how functional synergy between dynamically acting chromatin factors regulates nucleosome organization.
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Affiliation(s)
- Sandipan Brahma
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave North, Seattle, WA, 98109
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave North, Seattle, WA, 98109
- Howard Hughes Medical Institute, USA
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9
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Dubois A, Vincenti L, Chervova A, Greenberg MVC, Vandormael-Pournin S, Bourc'his D, Cohen-Tannoudji M, Navarro P. H3K9 tri-methylation at Nanog times differentiation commitment and enables the acquisition of primitive endoderm fate. Development 2022; 149:276335. [PMID: 35976266 PMCID: PMC9482333 DOI: 10.1242/dev.201074] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022]
Abstract
Mouse embryonic stem cells have an inherent propensity to explore gene regulatory states associated with either self-renewal or differentiation. This property depends on ERK, which downregulates pluripotency genes such as Nanog. Here, we aimed at identifying repressive histone modifications that would mark Nanog for inactivation in response to ERK activity. We found that the transcription factor ZFP57, which binds methylated DNA to nucleate heterochromatin, is recruited upstream of Nanog, within a region enriched for histone H3 lysine 9 tri-methylation (H3K9me3). Whereas before differentiation H3K9me3 at Nanog depends on ERK, in somatic cells it becomes independent of ERK. Moreover, the loss of H3K9me3 at Nanog, induced by deleting the region or by knocking out DNA methyltransferases or Zfp57, is associated with reduced heterogeneity of NANOG, delayed commitment into differentiation and impaired ability to acquire a primitive endoderm fate. Hence, a network axis centred on DNA methylation, ZFP57 and H3K9me3 links Nanog regulation to ERK activity for the timely establishment of new cell identities. We suggest that establishment of irreversible H3K9me3 at specific master regulators allows the acquisition of particular cell fates during differentiation. Summary: A regulatory axis integrating ERK, ZFP57, DNA and H3K9 methylation underlies the transition of Nanog expression from heterogeneous and dynamic to irreversibly silenced, enabling differentiation commitment and primitive endoderm specification.
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Affiliation(s)
- Agnès Dubois
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Loris Vincenti
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Almira Chervova
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Maxim V. C. Greenberg
- Department of Genetics and Developmental Biology, Institut Curie, PSL Research University, INSERM, CNRS 2 , 75005 Paris , France
- Université Paris Cité, CNRS, Institut Jacques Monod 3 , F-75013 Paris , France
| | - Sandrine Vandormael-Pournin
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Déborah Bourc'his
- Department of Genetics and Developmental Biology, Institut Curie, PSL Research University, INSERM, CNRS 2 , 75005 Paris , France
| | - Michel Cohen-Tannoudji
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
| | - Pablo Navarro
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit 1 Department of Developmental and Stem Cell Biology , , F-75015 Paris , France
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10
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Perera M, Nissen SB, Proks M, Pozzi S, Monteiro RS, Trusina A, Brickman JM. Transcriptional heterogeneity and cell cycle regulation as central determinants of primitive endoderm priming. eLife 2022; 11:78967. [PMID: 35969041 PMCID: PMC9417417 DOI: 10.7554/elife.78967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
During embryonic development cells acquire identity as they proliferate, implying that an intrinsic facet of cell fate choice requires coupling lineage decisions to cell division. How is the cell cycle regulated to promote or suppress heterogeneity and differentiation? We explore this question combining time lapse imaging with single-cell RNA-seq in the contexts of self-renewal, priming, and differentiation of mouse embryonic stem cells (ESCs) towards the Primitive Endoderm (PrE) lineage. Since ESCs are derived from the inner cell mass (ICM) of the mammalian blastocyst, ESCs in standard culture conditions are transcriptionally heterogeneous containing dynamically interconverting subfractions primed for either of the two ICM lineages, Epiblast and PrE. Here, we find that differential regulation of cell cycle can tip the balance between these primed populations, such that naïve ESC culture promotes Epiblast-like expansion and PrE differentiation stimulates the selective survival and proliferation of PrE-primed cells. In endoderm differentiation, this change is accompanied by a counter-intuitive increase in G1 length, also observed in vivo. While fibroblast growth factor/extracellular signal-regulated kinase (FGF/ERK) signalling is a key regulator of ESC differentiation and PrE specification, we find it is not just responsible for ESCs heterogeneity, but also the inheritance of similar cell cycles between sisters and cousins. Taken together, our results indicate a tight relationship between transcriptional heterogeneity and cell cycle regulation in lineage specification, with primed cell populations providing a pool of flexible cell types that can be expanded in a lineage-specific fashion while allowing plasticity during early determination.
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Affiliation(s)
- Marta Perera
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Martin Proks
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sara Pozzi
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rita Soares Monteiro
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
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11
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Seong J, Frias-Aldeguer J, Holzmann V, Kagawa H, Sestini G, Heidari Khoei H, Scholte Op Reimer Y, Kip M, Pradhan SJ, Verwegen L, Vivié J, Li L, Alemany A, Korving J, Darmis F, van Oudenaarden A, Ten Berge D, Geijsen N, Rivron NC. Epiblast inducers capture mouse trophectoderm stem cells in vitro and pattern blastoids for implantation in utero. Cell Stem Cell 2022; 29:1102-1118.e8. [PMID: 35803228 DOI: 10.1016/j.stem.2022.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/21/2022] [Accepted: 06/02/2022] [Indexed: 11/03/2022]
Abstract
The embryo instructs the allocation of cell states to spatially regulate functions. In the blastocyst, patterning of trophoblast (TR) cells ensures successful implantation and placental development. Here, we defined an optimal set of molecules secreted by the epiblast (inducers) that captures in vitro stable, highly self-renewing mouse trophectoderm stem cells (TESCs) resembling the blastocyst stage. When exposed to suboptimal inducers, these stem cells fluctuate to form interconvertible subpopulations with reduced self-renewal and facilitated differentiation, resembling peri-implantation cells, known as TR stem cells (TSCs). TESCs have enhanced capacity to form blastoids that implant more efficiently in utero due to inducers maintaining not only local TR proliferation and self-renewal, but also WNT6/7B secretion that stimulates uterine decidualization. Overall, the epiblast maintains sustained growth and decidualization potential of abutting TR cells, while, as known, distancing imposed by the blastocyst cavity differentiates TR cells for uterus adhesion, thus patterning the essential functions of implantation.
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Affiliation(s)
- Jinwoo Seong
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Javier Frias-Aldeguer
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands; Maastricht University, Maastricht, the Netherlands
| | - Viktoria Holzmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Harunobu Kagawa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Giovanni Sestini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Heidar Heidari Khoei
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria; Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Yvonne Scholte Op Reimer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Maarten Kip
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Saurabh J Pradhan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Lucas Verwegen
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Judith Vivié
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Linfeng Li
- Maastricht University, Maastricht, the Netherlands
| | - Anna Alemany
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Jeroen Korving
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | - Frank Darmis
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands
| | | | - Derk Ten Berge
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Niels Geijsen
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands; Department of Anatomy and Embryology, LUMC, Leiden University, Leiden, the Netherlands
| | - Nicolas C Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria; Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, the Netherlands; Maastricht University, Maastricht, the Netherlands.
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12
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Bioimaging approaches for quantification of individual cell behavior during cell fate decisions. Biochem Soc Trans 2022; 50:513-527. [PMID: 35166330 DOI: 10.1042/bst20210534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022]
Abstract
Tracking individual cells has allowed a new understanding of cellular behavior in human health and disease by adding a dynamic component to the already complex heterogeneity of single cells. Technically, despite countless advances, numerous experimental variables can affect data collection and interpretation and need to be considered. In this review, we discuss the main technical aspects and biological findings in the analysis of the behavior of individual cells. We discuss the most relevant contributions provided by these approaches in clinically relevant human conditions like embryo development, stem cells biology, inflammation, cancer and microbiology, along with the cellular mechanisms and molecular pathways underlying these conditions. We also discuss the key technical aspects to be considered when planning and performing experiments involving the analysis of individual cells over long periods. Despite the challenges in automatic detection, features extraction and long-term tracking that need to be tackled, the potential impact of single-cell bioimaging is enormous in understanding the pathogenesis and development of new therapies in human pathophysiology.
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13
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Springer C, Zakhartchenko V, Wolf E, Simmet K. Hypoblast Formation in Bovine Embryos Does Not Depend on NANOG. Cells 2021; 10:cells10092232. [PMID: 34571882 PMCID: PMC8466907 DOI: 10.3390/cells10092232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 12/24/2022] Open
Abstract
The role of the pluripotency factor NANOG during the second embryonic lineage differentiation has been studied extensively in mouse, although species-specific differences exist. To elucidate the role of NANOG in an alternative model organism, we knocked out NANOG in fibroblast cells and produced bovine NANOG-knockout (KO) embryos via somatic cell nuclear transfer (SCNT). At day 8, NANOG-KO blastocysts showed a decreased total cell number when compared to controls from SCNT (NT Ctrl). The pluripotency factors OCT4 and SOX2 as well as the hypoblast (HB) marker GATA6 were co-expressed in all cells of the inner cell mass (ICM) and, in contrast to mouse Nanog-KO, expression of the late HB marker SOX17 was still present. We blocked the MEK-pathway with a MEK 1/2 inhibitor, and control embryos showed an increase in NANOG positive cells, but SOX17 expressing HB precursor cells were still present. NANOG-KO together with MEK-inhibition was lethal before blastocyst stage, similarly to findings in mouse. Supplementation of exogenous FGF4 to NANOG-KO embryos did not change SOX17 expression in the ICM, unlike mouse Nanog-KO embryos, where missing SOX17 expression was completely rescued by FGF4. We conclude that NANOG mediated FGF/MEK signaling is not required for HB formation in the bovine embryo and that another—so far unknown—pathway regulates HB differentiation.
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Affiliation(s)
- Claudia Springer
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (C.S.); (V.Z.); (E.W.)
- Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany
| | - Valeri Zakhartchenko
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (C.S.); (V.Z.); (E.W.)
- Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (C.S.); (V.Z.); (E.W.)
- Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Kilian Simmet
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (C.S.); (V.Z.); (E.W.)
- Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany
- Correspondence:
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14
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Samanta T, Kar S. Fine-tuning Nanog expression heterogeneity in embryonic stem cells by regulating a Nanog transcript-specific microRNA. FEBS Lett 2020; 594:4292-4306. [PMID: 32969052 DOI: 10.1002/1873-3468.13936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 12/24/2022]
Abstract
In embryonic stem cells (ESCs), the transcription factor Nanog maintains the stemness of ESCs despite exhibiting heterogeneous expression patterns under varied culture conditions. Efficient fine-tuning of Nanog expression heterogeneity could enable ESC proliferation and differentiation along specific lineages to be regulated. Herein, by employing a stochastic modeling approach, we show that Nanog expression heterogeneity can be controlled by modulating the regulatory features of a Nanog transcript-specific microRNA, mir-296. We demonstrate how and why the extent of origin-dependent fluctuations in Nanog expression level can be altered by varying either the binding efficiency of the microRNA-mRNA complex or the expression level of mir-296. Moreover, our model makes experimentally feasible and insightful predictions to maneuver Nanog expression heterogeneity explicitly to achieve cell-type-specific differentiation of ESCs.
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Affiliation(s)
| | - Sandip Kar
- Department of Chemistry, IIT Bombay, Mumbai, India
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15
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Abstract
In this issue of Stem Cell Reports, Hastreiter et al. (2018) use continuous time-lapse imaging of mouse embryonic stem cells to investigate how the inhibition of GSK3b and MEK/ERK (2i) leads to homogeneous expression of the transcription factor Nanog. They show that both induction of Nanog expression and selection against cells expressing low levels of Nanog contribute to the homogeneous appearance of 2i cultures.
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Affiliation(s)
- Pablo Navarro
- Epigenetics of Stem Cells, Department of Developmental & Stem Cell Biology, Institut Pasteur, CNRS UMR 3738, 25 rue du docteur Roux, 75015 Paris, France.
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16
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Ritter A, Kreis NN, Roth S, Friemel A, Jennewein L, Eichbaum C, Solbach C, Louwen F, Yuan J. Restoration of primary cilia in obese adipose-derived mesenchymal stem cells by inhibiting Aurora A or extracellular signal-regulated kinase. Stem Cell Res Ther 2019; 10:255. [PMID: 31412932 PMCID: PMC6694567 DOI: 10.1186/s13287-019-1373-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Obesity impairs a variety of cell types including adipose-derived mesenchymal stem cells (ASCs). ASCs are indispensable for tissue homeostasis/repair, immunomodulation, and cell renewal. It has been demonstrated that obese ASCs are defective in differentiation, motility, immunomodulation, and replication. We have recently reported that some of these defects are linked to impaired primary cilia, which are unable to properly convey and coordinate a variety of signaling pathways. We hypothesized that the rescue of the primary cilium in obese ASCs would restore their functional properties. METHODS Obese ASCs derived from subcutaneous and visceral adipose tissues were treated with a specific inhibitor against Aurora A or with an inhibitor against extracellular signal-regulated kinase 1/2 (Erk1/2). Multiple molecular and cellular assays were performed to analyze the altered functionalities and their involved pathways. RESULTS The treatment with low doses of these inhibitors extended the length of the primary cilium, restored the invasion and migration potential, and improved the differentiation capacity of obese ASCs. Associated with enhanced differentiation ability, the cells displayed an increased expression of self-renewal/stemness-related genes like SOX2, OCT4, and NANOG, mediated by reduced active glycogen synthase kinase 3 β (GSK3β). CONCLUSION This work describes a novel phenomenon whereby the primary cilium of obese ASCs is rescuable by the low-dose inhibition of Aurora A or Erk1/2, restoring functional ASCs with increased stemness. These cells might be able to improve tissue homeostasis in obese patients and thereby ameliorate obesity-associated diseases. Additionally, these functionally restored obese ASCs could be useful for novel autologous mesenchymal stem cell-based therapies.
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Affiliation(s)
- Andreas Ritter
- Department of Gynecology and Obstetrics, School of Medicine, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590, Frankfurt, Germany.
| | - Nina-Naomi Kreis
- Department of Gynecology and Obstetrics, School of Medicine, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590, Frankfurt, Germany
| | - Susanne Roth
- Department of Gynecology and Obstetrics, School of Medicine, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590, Frankfurt, Germany
| | - Alexandra Friemel
- Department of Gynecology and Obstetrics, School of Medicine, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590, Frankfurt, Germany
| | - Lukas Jennewein
- Department of Gynecology and Obstetrics, School of Medicine, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590, Frankfurt, Germany
| | - Christine Eichbaum
- Department of Gynecology and Obstetrics, School of Medicine, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590, Frankfurt, Germany
| | - Christine Solbach
- Department of Gynecology and Obstetrics, School of Medicine, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590, Frankfurt, Germany
| | - Frank Louwen
- Department of Gynecology and Obstetrics, School of Medicine, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590, Frankfurt, Germany
| | - Juping Yuan
- Department of Gynecology and Obstetrics, School of Medicine, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590, Frankfurt, Germany.
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17
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Extensive epigenetic and transcriptomic variability between genetically identical human B-lymphoblastoid cells with implications in pharmacogenomics research. Sci Rep 2019; 9:4889. [PMID: 30894562 PMCID: PMC6426863 DOI: 10.1038/s41598-019-40897-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/20/2019] [Indexed: 12/12/2022] Open
Abstract
Genotyped human B-lymphoblastoid cell lines (LCLs) are widely used models in mapping quantitative trait loci for chromatin features, gene expression, and drug response. The extent of genotype-independent functional genomic variability of the LCL model, although largely overlooked, may inform association study design. In this study, we use flow cytometry, chromatin immunoprecipitation sequencing and mRNA sequencing to study surface marker patterns, quantify genome-wide chromatin changes (H3K27ac) and transcriptome variability, respectively, among five isogenic LCLs derived from the same individual. Most of the studied LCLs were non-monoclonal and had mature B cell phenotypes. Strikingly, nearly one-fourth of active gene regulatory regions showed significantly variable H3K27ac levels, especially enhancers, among which several were classified as clustered enhancers. Large, contiguous genomic regions showed signs of coordinated activity change. Regulatory differences were mirrored by mRNA expression changes, preferentially affecting hundreds of genes involved in specialized cellular processes including immune and drug response pathways. Differential expression of DPYD, an enzyme involved in 5-fluorouracil (5-FU) catabolism, was associated with variable LCL growth inhibition mediated by 5-FU. The extent of genotype-independent functional genomic variability might highlight the need to revisit study design strategies for LCLs in pharmacogenomics.
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18
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Festuccia N, Halbritter F, Corsinotti A, Gagliardi A, Colby D, Tomlinson SR, Chambers I. Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation. EMBO J 2018; 37:e95476. [PMID: 30275266 PMCID: PMC6213284 DOI: 10.15252/embj.201695476] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 11/25/2022] Open
Abstract
Self-renewal of embryonic stem cells (ESCs) cultured in LIF/fetal calf serum (FCS) is incomplete with some cells initiating differentiation. While this is reflected in heterogeneous expression of naive pluripotency transcription factors (TFs), the link between TF heterogeneity and differentiation is not fully understood. Here, we purify ESCs with distinct TF expression levels from LIF/FCS cultures to uncover early events during commitment from naïve pluripotency. ESCs carrying fluorescent Nanog and Esrrb reporters show Esrrb downregulation only in Nanoglow cells. Independent Esrrb reporter lines demonstrate that Esrrbnegative ESCs cannot effectively self-renew. Upon Esrrb loss, pre-implantation pluripotency gene expression collapses. ChIP-Seq identifies different regulatory element classes that bind both OCT4 and NANOG in Esrrbpositive cells. Class I elements lose NANOG and OCT4 binding in Esrrbnegative ESCs and associate with genes expressed preferentially in naïve ESCs. In contrast, Class II elements retain OCT4 but not NANOG binding in ESRRB-negative cells and associate with more broadly expressed genes. Therefore, mechanistic differences in TF function act cumulatively to restrict potency during exit from naïve pluripotency.
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Affiliation(s)
- Nicola Festuccia
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Florian Halbritter
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Andrea Corsinotti
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Alessia Gagliardi
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Douglas Colby
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Simon R Tomlinson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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