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Song C, Zhang Z, Leng D, He Z, Wang X, Liu W, Zhang W, Wu Q, Zhao Q, Chen G. ERK5 promotes autocrine expression to sustain mitogenic balance for cell fate specification in human pluripotent stem cells. Stem Cell Reports 2024:S2213-6711(24)00216-9. [PMID: 39151429 DOI: 10.1016/j.stemcr.2024.07.007] [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: 11/28/2023] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024] Open
Abstract
The homeostasis of human pluripotent stem cells (hPSCs) requires the signaling balance of extracellular factors. Exogenous regulators from cell culture medium have been widely reported, but little attention has been paid to the autocrine factor from hPSCs themselves. In this report, we demonstrate that extracellular signal-related kinase 5 (ERK5) regulates endogenous autocrine factors essential for pluripotency and differentiation. ERK5 inhibition leads to erroneous cell fate specification in all lineages even under lineage-specific induction. hPSCs can self-renew under ERK5 inhibition in the presence of fibroblast growth factor 2 (FGF2) and transforming growth factor β (TGF-β), although NANOG expression is partially suppressed. Further analysis demonstrates that ERK5 promotes the expression of autocrine factors such as NODAL, FGF8, and WNT3. The addition of NODAL protein rescues NANOG expression and differentiation phenotypes under ERK5 inhibition. We demonstrate that constitutively active ERK5 pathway allows self-renewal even without essential growth factors FGF2 and TGF-β. This study highlights the essential contribution of autocrine pathways to proper maintenance and differentiation.
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Affiliation(s)
- Chengcheng Song
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Zhaoying Zhang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Dongliang Leng
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Ziqing He
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Xuepeng Wang
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, China; CAM-SU Genomic Resource Center, Soochow University, Suzhou, Jiangsu, China
| | - Weiwei Liu
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Biological Imaging and Stem Cell Core Facility, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Wensheng Zhang
- CAM-SU Genomic Resource Center, Soochow University, Suzhou, Jiangsu, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau, China
| | - Qi Zhao
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Zhuhai UM Science & Technology Research Institute, Zhuhai, China.
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2
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Saha D, Animireddy S, Bartholomew B. The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development. Biochem Soc Trans 2024; 52:603-616. [PMID: 38572912 PMCID: PMC11088921 DOI: 10.1042/bst20230416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins. In development, SWI/SNF orchestrates the precise activation and repression of genes at different stages, safe guards the formation of specific cell lineages and tissues. Dysregulation of SWI/SNF have been implicated in diseases such as cancer, where they can drive uncontrolled cell proliferation and tumor metastasis. Additionally, SWI/SNF defects are associated with neurodevelopmental disorders, leading to disruption of neural development and function. This review offers insights into recent developments regarding the roles of the SWI/SNF complex in pluripotency and cell lineage primining and the approaches that have helped delineate its importance. Understanding these molecular mechanisms is crucial for unraveling the intricate processes governing embryonic stem cell biology and developmental transitions and may potentially apply to human diseases linked to mutations in the SWI/SNF complex.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
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3
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Hook PW, Timp W. Beyond assembly: the increasing flexibility of single-molecule sequencing technology. Nat Rev Genet 2023; 24:627-641. [PMID: 37161088 PMCID: PMC10169143 DOI: 10.1038/s41576-023-00600-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, including filling gaps in the human reference genome, measuring the epigenome and characterizing splicing variants in the transcriptome. With recent technological developments, these single-molecule technologies have moved beyond genome assembly and are being used in a variety of ways, including to selectively sequence specific loci with long reads, measure chromatin state and protein-DNA binding in order to investigate the dynamics of gene regulation, and rapidly determine copy number variation. These increasingly flexible uses of single-molecule technologies highlight a young and fast-moving part of the field that is leading to a more accessible era of nucleic acid sequencing.
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Affiliation(s)
- Paul W Hook
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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4
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Baur B, Shin J, Schreiber J, Zhang S, Zhang Y, Manjunath M, Song JS, Stafford Noble W, Roy S. Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation. PLoS Comput Biol 2023; 19:e1011286. [PMID: 37428809 PMCID: PMC10358954 DOI: 10.1371/journal.pcbi.1011286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 06/20/2023] [Indexed: 07/12/2023] Open
Abstract
Understanding the impact of regulatory variants on complex phenotypes is a significant challenge because the genes and pathways that are targeted by such variants and the cell type context in which regulatory variants operate are typically unknown. Cell-type-specific long-range regulatory interactions that occur between a distal regulatory sequence and a gene offer a powerful framework for examining the impact of regulatory variants on complex phenotypes. However, high-resolution maps of such long-range interactions are available only for a handful of cell types. Furthermore, identifying specific gene subnetworks or pathways that are targeted by a set of variants is a significant challenge. We have developed L-HiC-Reg, a Random Forests regression method to predict high-resolution contact counts in new cell types, and a network-based framework to identify candidate cell-type-specific gene networks targeted by a set of variants from a genome-wide association study (GWAS). We applied our approach to predict interactions in 55 Roadmap Epigenomics Mapping Consortium cell types, which we used to interpret regulatory single nucleotide polymorphisms (SNPs) in the NHGRI-EBI GWAS catalogue. Using our approach, we performed an in-depth characterization of fifteen different phenotypes including schizophrenia, coronary artery disease (CAD) and Crohn's disease. We found differentially wired subnetworks consisting of known as well as novel gene targets of regulatory SNPs. Taken together, our compendium of interactions and the associated network-based analysis pipeline leverages long-range regulatory interactions to examine the context-specific impact of regulatory variation in complex phenotypes.
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Affiliation(s)
- Brittany Baur
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Junha Shin
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jacob Schreiber
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
| | - Shilu Zhang
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Yi Zhang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Mohith Manjunath
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jun S Song
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - William Stafford Noble
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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5
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Hussein AM, Balachandar N, Mathieu J, Ruohola-Baker H. Molecular Regulators of Embryonic Diapause and Cancer Diapause-like State. Cells 2022; 11:cells11192929. [PMID: 36230891 PMCID: PMC9562880 DOI: 10.3390/cells11192929] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Embryonic diapause is an enigmatic state of dormancy that interrupts the normally tight connection between developmental stages and time. This reproductive strategy and state of suspended development occurs in mice, bears, roe deer, and over 130 other mammals and favors the survival of newborns. Diapause arrests the embryo at the blastocyst stage, delaying the post-implantation development of the embryo. This months-long quiescence is reversible, in contrast to senescence that occurs in aging stem cells. Recent studies have revealed critical regulators of diapause. These findings are important since defects in the diapause state can cause a lack of regeneration and control of normal growth. Controlling this state may also have therapeutic applications since recent findings suggest that radiation and chemotherapy may lead some cancer cells to a protective diapause-like, reversible state. Interestingly, recent studies have shown the metabolic regulation of epigenetic modifications and the role of microRNAs in embryonic diapause. In this review, we discuss the molecular mechanism of diapause induction.
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Affiliation(s)
- Abdiasis M. Hussein
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Nanditaa Balachandar
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Chennai 603203, India
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Department of Comparative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Correspondence:
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6
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Epigenetics as "conductor" in "orchestra" of pluripotent states. Cell Tissue Res 2022; 390:141-172. [PMID: 35838826 DOI: 10.1007/s00441-022-03667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Pluripotent character is described as the potency of cells to differentiate into all three germ layers. The best example to reinstate the term lies in the context of embryonic stem cells (ESCs). Pluripotent ESC describes the in vitro status of those cells that originate during the complex process of embryogenesis. Pre-implantation to post-implantation development of embryo embrace cells with different levels of stemness. Currently, four states of pluripotency have been recognized, in the progressing order of "naïve," "poised," "formative," and "primed." Epigenetics act as the "conductor" in this "orchestra" of transition in pluripotent states. With a distinguishable gene expression profile, these four states associate with different epigenetic signatures, sometimes distinct while otherwise overlapping. The present review focuses on how epigenetic factors, including DNA methylation, bivalent chromatin, chromatin remodelers, chromatin/nuclear architecture, and microRNA, could dictate pluripotent states and their transition among themselves.
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7
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Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction. Nat Cell Biol 2022; 24:858-871. [PMID: 35697783 PMCID: PMC9203278 DOI: 10.1038/s41556-022-00932-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
Abstract
Human naive pluripotent stem cells have unrestricted lineage potential. Underpinning this property, naive cells are thought to lack chromatin-based lineage barriers. However, this assumption has not been tested. Here we define the chromatin-associated proteome, histone post-translational modifications and transcriptome of human naive and primed pluripotent stem cells. Our integrated analysis reveals differences in the relative abundance and activities of distinct chromatin modules. We identify a strong enrichment of polycomb repressive complex 2 (PRC2)-associated H3K27me3 in the chromatin of naive pluripotent stem cells and H3K27me3 enrichment at promoters of lineage-determining genes, including trophoblast regulators. PRC2 activity acts as a chromatin barrier restricting the differentiation of naive cells towards the trophoblast lineage, whereas inhibition of PRC2 promotes trophoblast-fate induction and cavity formation in human blastoids. Together, our results establish that human naive pluripotent stem cells are not epigenetically unrestricted, but instead possess chromatin mechanisms that oppose the induction of alternative cell fates. Two side-by-side papers report that H3K27me3 deposited by polycomb repressive complex 2 represents an epigenetic barrier that restricts naive human pluripotent cell differentiation into alternative lineages including trophoblasts.
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8
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Kumar B, Navarro C, Winblad N, Schell JP, Zhao C, Weltner J, Baqué-Vidal L, Salazar Mantero A, Petropoulos S, Lanner F, Elsässer SJ. Polycomb repressive complex 2 shields naïve human pluripotent cells from trophectoderm differentiation. Nat Cell Biol 2022; 24:845-857. [PMID: 35637409 PMCID: PMC9203276 DOI: 10.1038/s41556-022-00916-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/13/2022] [Indexed: 12/12/2022]
Abstract
The first lineage choice in human embryo development separates trophectoderm from the inner cell mass. Naïve human embryonic stem cells are derived from the inner cell mass and offer possibilities to explore how lineage integrity is maintained. Here, we discover that polycomb repressive complex 2 (PRC2) maintains naïve pluripotency and restricts differentiation to trophectoderm and mesoderm lineages. Through quantitative epigenome profiling, we found that a broad gain of histone H3 lysine 27 trimethylation (H3K27me3) is a distinct feature of naïve pluripotency. We define shared and naïve-specific bivalent promoters featuring PRC2-mediated H3K27me3 concomitant with H3K4me3. Naïve bivalency maintains key trophectoderm and mesoderm transcription factors in a transcriptionally poised state. Inhibition of PRC2 forces naïve human embryonic stem cells into an ‘activated’ state, characterized by co-expression of pluripotency and lineage-specific transcription factors, followed by differentiation into either trophectoderm or mesoderm lineages. In summary, PRC2-mediated repression provides a highly adaptive mechanism to restrict lineage potential during early human development. Two side-by-side papers report that H3K27me3 deposited by polycomb repressive complex 2 represents an epigenetic barrier that restricts naïve human pluripotent cell differentiation into alternative lineages including trophoblasts.
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9
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Levy S, Somasundaram L, Raj IX, Ic-Mex D, Phal A, Schmidt S, Ng WI, Mar D, Decarreau J, Moss N, Alghadeer A, Honkanen H, Sarthy J, Vitanza N, Hawkins RD, Mathieu J, Wang Y, Baker D, Bomsztyk K, Ruohola-Baker H. dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region. Cell Rep 2022; 38:110457. [PMID: 35235780 PMCID: PMC8984963 DOI: 10.1016/j.celrep.2022.110457] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 11/23/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Bifurcation of cellular fates, a critical process in development, requires histone 3 lysine 27 methylation (H3K27me3) marks propagated by the polycomb repressive complex 2 (PRC2). However, precise chromatin loci of functional H3K27me3 marks are not yet known. Here, we identify critical PRC2 functional sites at high resolution. We fused a computationally designed protein, EED binder (EB), which competes with EZH2 and thereby inhibits PRC2 function, to dCas9 (EBdCas9) to allow for PRC2 inhibition at a precise locus using gRNA. Targeting EBdCas9 to four different genes (TBX18, p16, CDX2, and GATA3) results in precise H3K27me3 and EZH2 reduction, gene activation, and functional outcomes in the cell cycle (p16) or trophoblast transdifferentiation (CDX2 and GATA3). In the case of TBX18, we identify a PRC2-controlled, functional TATA box >500 bp upstream of the TBX18 transcription start site (TSS) using EBdCas9. Deletion of this TATA box eliminates EBdCas9-dependent TATA binding protein (TBP) recruitment and transcriptional activation. EBdCas9 technology may provide a broadly applicable tool for epigenomic control of gene regulation. Levy et al. fused a computationally designed protein, EED binder (EB), which competes with EZH2 and thereby inhibits PRC2 function, to dCas9 (EBdCas9). EBdCas9 represses PRC2 action in precise loci, remodels epigenomic marks, exposes transcriptional elements, and induces transdifferentiation.
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Affiliation(s)
- Shiri Levy
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Logeshwaran Somasundaram
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Infencia Xavier Raj
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Diego Ic-Mex
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Ashish Phal
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, School of Medicine, Seattle, WA 98105, USA
| | - Sven Schmidt
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Weng I Ng
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Daniel Mar
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA 98195, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Moss
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Division of Medical Genetics, Department of Medicine, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ammar Alghadeer
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98109, USA; Department of Biomedical Dental Sciences, Imam Abdulrahman Bin Faisal University, College of Dentistry, Dammam 31441, Saudi Arabia
| | - Henrik Honkanen
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Jay Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorder Center, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Nicholas Vitanza
- The Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - R David Hawkins
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Division of Medical Genetics, Department of Medicine, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Karol Bomsztyk
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA 98195, USA
| | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, School of Medicine, Seattle, WA 98105, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98109, USA.
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10
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Bendall A, Semprich CI. Chromatin Profiling of Human Naïve Pluripotent Stem Cells. Methods Mol Biol 2022; 2416:181-200. [PMID: 34870837 DOI: 10.1007/978-1-0716-1908-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-sequencing) facilitates the genome-wide mapping of DNA sequences that are enriched for specific chromatin-binding proteins or histone post-translational modifications. More recently developed chromatin profiling methods called Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and Cleavage Under Targets and Tagmentation (CUT&Tag) have adapted the ChIP-sequencing approach to produce similar data from a smaller amount of starting material, and while overcoming many of the conventional drawbacks of ChIP-sequencing. Here, we present detailed protocols for ChIP-seq, CUT&RUN, and CUT&Tag to profile genome-wide protein-DNA interactions in naïve human pluripotent stem cells.
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Affiliation(s)
- Adam Bendall
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
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11
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Hassanaly-Goulamhoussen R, De Carvalho Augusto R, Marteu-Garello N, Péré A, Favery B, Da Rocha M, Danchin EGJ, Abad P, Grunau C, Perfus-Barbeoch L. Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita. Front Cell Dev Biol 2021; 9:765690. [PMID: 34938734 PMCID: PMC8685519 DOI: 10.3389/fcell.2021.765690] [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: 08/27/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
In model organisms, epigenome dynamics underlies a plethora of biological processes. The role of epigenetic modifications in development and parasitism in nematode pests remains unknown. The root-knot nematode Meloidogyne incognita adapts rapidly to unfavorable conditions, despite its asexual reproduction. However, the mechanisms underlying this remarkable plasticity and their potential impact on gene expression remain unknown. This study provides the first insight into contribution of epigenetic mechanisms to this plasticity, by studying histone modifications in M. incognita. The distribution of five histone modifications revealed the existence of strong epigenetic signatures, similar to those found in the model nematode Caenorhabditis elegans. We investigated their impact on chromatin structure and their distribution relative to transposable elements (TE) loci. We assessed the influence of the chromatin landscape on gene expression at two developmental stages: eggs, and pre-parasitic juveniles. H3K4me3 histone modification was strongly correlated with high levels of expression for protein-coding genes implicated in stage-specific processes during M. incognita development. We provided new insights in the dynamic regulation of parasitism genes kept under histone modifications silencing. In this pioneering study, we establish a comprehensive framework for the importance of epigenetic mechanisms in the regulation of the genome expression and its stability in plant-parasitic nematodes.
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Affiliation(s)
| | - Ronaldo De Carvalho Augusto
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, France.,Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | | | - Arthur Péré
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Bruno Favery
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Martine Da Rocha
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | | | - Pierre Abad
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Christoph Grunau
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, France
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12
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Yang W, Wang P, Cao P, Wang S, Yang Y, Su H, Nashun B. Hypoxic in vitro culture reduces histone lactylation and impairs pre-implantation embryonic development in mice. Epigenetics Chromatin 2021; 14:57. [PMID: 34930415 PMCID: PMC8691063 DOI: 10.1186/s13072-021-00431-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Dynamic changes of histone posttranslational modifications are important contexts of epigenetic reprograming after fertilization in pre-implantation embryos. Recently, lactylation has been reported as a novel epigenetic modification that regulates various cellular processes, but its role during early embryogenesis has not been elucidated. RESULTS We examined nuclear accumulation of H3K23la, H3K18la and pan histone lactylation in mouse oocytes and pre-implantation embryos by immunofluorescence with specific antibodies. All of the three modifications were abundant in GV stage oocytes, and both H3K23la and pan histone lactylation could be detected on the condensed chromosomes of the MII oocytes, while H3K18la were not detected. After fertilization, the nuclear staining of H3K23la, H3K18la and pan histone lactylation was faint in zygotes but homogeneously stained both of the parental pronuclei. The signal remained weak in the early cleavage stage embryos and increased remarkably in the blastocyst stage embryos. Comparison of the embryos cultured in four different conditions with varying concentrations of oxygen found that H3K23la, H3K18la and pan histone lactylation showed similar and comparable staining pattern in embryos cultured in atmospheric oxygen concentration (20% O2), gradient oxygen concentration (5% O2 to 2% O2) and embryos obtained from in vivo, but the modifications were greatly reduced in embryos cultured in hypoxic condition (2% O2). In contrast, nuclear accumulation of H3K18ac or H3K23ac was not significantly affected under hypoxic condition. Moreover, the developmental rate of in vitro cultured embryo was significantly reduced by low oxygen concentration and small molecule inhibition of LDHA activity led to decreased lactate production, as well as reduced histone lactylation and compromised developmental rate. CONCLUSIONS We provided for the first time the dynamic landscape of H3K23la, H3K18la and pan histone lactylation in oocytes and pre-implantation embryos in mice. Our data suggested that histone lactylation is subjected to oxygen concentration in the culture environment and hypoxic in vitro culture reduces histone lactylation, which in turn compromises developmental potential of pre-implantation embryos in mice.
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Affiliation(s)
- Wanting Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Peijun Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Pengbo Cao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Shuang Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yuxiao Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Huimin Su
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Buhe Nashun
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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13
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Sanghi A, Gruber JJ, Metwally A, Jiang L, Reynolds W, Sunwoo J, Orloff L, Chang HY, Kasowski M, Snyder MP. Chromatin accessibility associates with protein-RNA correlation in human cancer. Nat Commun 2021; 12:5732. [PMID: 34593797 PMCID: PMC8484618 DOI: 10.1038/s41467-021-25872-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 08/24/2021] [Indexed: 11/19/2022] Open
Abstract
Although alterations in chromatin structure are known to exist in tumors, how these alterations relate to molecular phenotypes in cancer remains to be demonstrated. Multi-omics profiling of human tumors can provide insight into how alterations in chromatin structure are propagated through the pathway of gene expression to result in malignant protein expression. We applied multi-omics profiling of chromatin accessibility, RNA abundance, and protein abundance to 36 human thyroid cancer primary tumors, metastases, and patient-match normal tissue. Through quantification of chromatin accessibility associated with active transcription units and global protein expression, we identify a local chromatin structure that is highly correlated with coordinated RNA and protein expression. In particular, we identify enhancers located within gene-bodies as predictive of correlated RNA and protein expression, that is independent of overall transcriptional activity. To demonstrate the generalizability of these findings we also identify similar results in an independent cohort of human breast cancers. Taken together, these analyses suggest that local enhancers, rather than distal enhancers, are likely most predictive of cancer gene expression phenotypes. This allows for identification of potential targets for cancer therapeutic approaches and reinforces the utility of multi-omics profiling as a methodology to understand human disease.
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Affiliation(s)
- Akshay Sanghi
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Joshua J Gruber
- Department of Genetics, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Ahmed Metwally
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Warren Reynolds
- Center for Personal Dynamic Regulomes and HHMI, Stanford University, Stanford, USA
| | - John Sunwoo
- Division of Head and Neck Surgery, Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Orloff
- Division of Head and Neck Surgery, Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes and HHMI, Stanford University, Stanford, USA
| | - Maya Kasowski
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford University, Stanford, CA, USA
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14
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Osnato A, Brown S, Krueger C, Andrews S, Collier AJ, Nakanoh S, Quiroga Londoño M, Wesley BT, Muraro D, Brumm AS, Niakan KK, Vallier L, Ortmann D, Rugg-Gunn PJ. TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells. eLife 2021; 10:e67259. [PMID: 34463252 PMCID: PMC8410071 DOI: 10.7554/elife.67259] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/26/2021] [Indexed: 12/30/2022] Open
Abstract
The signalling pathways that maintain primed human pluripotent stem cells (hPSCs) have been well characterised, revealing a critical role for TGFβ/Activin/Nodal signalling. In contrast, the signalling requirements of naive human pluripotency have not been fully established. Here, we demonstrate that TGFβ signalling is required to maintain naive hPSCs. The downstream effector proteins - SMAD2/3 - bind common sites in naive and primed hPSCs, including shared pluripotency genes. In naive hPSCs, SMAD2/3 additionally bind to active regulatory regions near to naive pluripotency genes. Inhibiting TGFβ signalling in naive hPSCs causes the downregulation of SMAD2/3-target genes and pluripotency exit. Single-cell analyses reveal that naive and primed hPSCs follow different transcriptional trajectories after inhibition of TGFβ signalling. Primed hPSCs differentiate into neuroectoderm cells, whereas naive hPSCs transition into trophectoderm. These results establish that there is a continuum for TGFβ pathway function in human pluripotency spanning a developmental window from naive to primed states.
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Affiliation(s)
- Anna Osnato
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Stephanie Brown
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Christel Krueger
- Bioinformatics Group, The Babraham InstituteCambridgeUnited Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham InstituteCambridgeUnited Kingdom
| | - Amanda J Collier
- Epigenetics Programme, The Babraham InstituteCambridgeUnited Kingdom
| | - Shota Nakanoh
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
- Division of Embryology, National Institute for Basic BiologyOkazakiJapan
| | - Mariana Quiroga Londoño
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Brandon T Wesley
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Daniele Muraro
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger Institute, HinxtonCambridgeUnited Kingdom
| | - A Sophie Brumm
- Human Embryo and Stem Cell Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Centre for Trophoblast Research, University of CambridgeCambridgeUnited Kingdom
| | - Ludovic Vallier
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Daniel Ortmann
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Peter J Rugg-Gunn
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Epigenetics Programme, The Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast Research, University of CambridgeCambridgeUnited Kingdom
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15
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Sexton CE, Tillett RL, Han MV. The essential but enigmatic regulatory role of HERVH in pluripotency. Trends Genet 2021; 38:12-21. [PMID: 34340871 DOI: 10.1016/j.tig.2021.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 01/09/2023]
Abstract
Human specific endogenous retrovirus H (HERVH) is highly expressed in both naive and primed stem cells and is essential for pluripotency. Despite the proven relationship between HERVH expression and pluripotency, there is no single definitive model for the function of HERVH. Instead, several hypotheses of a regulatory function have been put forward including HERVH acting as enhancers, long noncoding RNAs (lncRNAs), and most recently as markers of topologically associating domain (TAD) boundaries. Recently several enhancer-associated lncRNAs have been characterized, which bind to Mediator and are necessary for promoter-enhancer folding interactions. We propose a synergistic model of HERVH function combining relevant findings and discuss the current limitations for its role in regulation, including the lack of evidence for a pluripotency-associated target gene.
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Affiliation(s)
- Corinne E Sexton
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | | | - Mira V Han
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, Las Vegas, NV 89154, USA.
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16
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Gong H, Yang Y, Zhang S, Li M, Zhang X. Application of Hi-C and other omics data analysis in human cancer and cell differentiation research. Comput Struct Biotechnol J 2021; 19:2070-2083. [PMID: 33995903 PMCID: PMC8086027 DOI: 10.1016/j.csbj.2021.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/04/2021] [Accepted: 04/04/2021] [Indexed: 02/07/2023] Open
Abstract
With the development of 3C (chromosome conformation capture) and its derivative technology Hi-C (High-throughput chromosome conformation capture) research, the study of the spatial structure of the genomic sequence in the nucleus helps researchers understand the functions of biological processes such as gene transcription, replication, repair, and regulation. In this paper, we first introduce the research background and purpose of Hi-C data visualization analysis. After that, we discuss the Hi-C data analysis methods from genome 3D structure, A/B compartment, TADs (topologically associated domain), and loop detection. We also discuss how to apply genome visualization technologies to the identification of chromosome feature structures. We continue with a review of correlation analysis differences among multi-omics data, and how to apply Hi-C and other omics data analysis into cancer and cell differentiation research. Finally, we summarize the various problems in joint analyses based on Hi-C and other multi-omics data. We believe this review can help researchers better understand the progress and applications of 3D genome technology.
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Affiliation(s)
- Haiyan Gong
- Department of Computer Science and Technology, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing 100083, China
- Shunde Graduate School of University of Science and Technology Beijing, Foshan 528000, China
| | - Yi Yang
- Department of Computer Science and Technology, University of Science and Technology Beijing, Beijing 100083, China
| | - Sichen Zhang
- Department of Computer Science and Technology, University of Science and Technology Beijing, Beijing 100083, China
| | - Minghong Li
- Department of Computer Science and Technology, University of Science and Technology Beijing, Beijing 100083, China
| | - Xiaotong Zhang
- Department of Computer Science and Technology, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing 100083, China
- Shunde Graduate School of University of Science and Technology Beijing, Foshan 528000, China
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17
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Chovanec P, Collier AJ, Krueger C, Várnai C, Semprich CI, Schoenfelder S, Corcoran AE, Rugg-Gunn PJ. Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states. Nat Commun 2021; 12:2098. [PMID: 33828098 PMCID: PMC8026613 DOI: 10.1038/s41467-021-22201-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 03/05/2021] [Indexed: 01/10/2023] Open
Abstract
The transition from naive to primed pluripotency is accompanied by an extensive reorganisation of transcriptional and epigenetic programmes. However, the role of transcriptional enhancers and three-dimensional chromatin organisation in coordinating these developmental programmes remains incompletely understood. Here, we generate a high-resolution atlas of gene regulatory interactions, chromatin profiles and transcription factor occupancy in naive and primed human pluripotent stem cells, and develop a network-graph approach to examine the atlas at multiple spatial scales. We uncover highly connected promoter hubs that change substantially in interaction frequency and in transcriptional co-regulation between pluripotent states. Small hubs frequently merge to form larger networks in primed cells, often linked by newly-formed Polycomb-associated interactions. We identify widespread state-specific differences in enhancer activity and interactivity that correspond with an extensive reconfiguration of OCT4, SOX2 and NANOG binding and target gene expression. These findings provide multilayered insights into the chromatin-based gene regulatory control of human pluripotent states.
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Affiliation(s)
- Peter Chovanec
- Lymphocyte Signalling and Development Programme, Babraham Institute, Cambridge, UK
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | | | - Stefan Schoenfelder
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Anne E Corcoran
- Lymphocyte Signalling and Development Programme, Babraham Institute, Cambridge, UK
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
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18
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McKee C, Brown C, Bakshi S, Walker K, Govind CK, Chaudhry GR. Transcriptomic Analysis of Naïve Human Embryonic Stem Cells Cultured in Three-Dimensional PEG Scaffolds. Biomolecules 2020; 11:E21. [PMID: 33379237 PMCID: PMC7824559 DOI: 10.3390/biom11010021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/24/2020] [Indexed: 12/21/2022] Open
Abstract
Naïve human embryonic stem cells (ESCs) are characterized by improved viability, proliferation, and differentiation capacity in comparison to traditionally derived primed human ESCs. However, currently used two-dimensional (2-D) cell culture techniques fail to mimic the three-dimensional (3-D) in vivo microenvironment, altering morphological and molecular characteristics of ESCs. Here, we describe the use of 3-D self-assembling scaffolds that support growth and maintenance of the naïve state characteristics of ESC line, Elf1. Scaffolds were formed via a Michael addition reaction upon the combination of two 8-arm polyethylene glycol (PEG) polymers functionalized with thiol (PEG-8-SH) and acrylate (PEG-8-Acr) end groups. 3-D scaffold environment maintained the naïve state and supported the long-term growth of ESCs. RNA-sequencing demonstrated significant changes in gene expression profiles between 2-D and 3-D grown cells. Gene ontology analysis revealed upregulation of biological processes involved in the regulation of transcription and translation, extracellular matrix organization, and chromatin remodeling in 3-D grown cells. 3-D culture conditions also induced upregulation of genes associated with Wnt and focal adhesion signaling, while p53 signaling pathway associated genes were downregulated. Our findings, for the first time, provide insight into the possible mechanisms of self-renewal of naïve ESCs stimulated by the transduction of mechanical signals from the 3-D microenvironment.
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Affiliation(s)
- Christina McKee
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - Christina Brown
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - Shreeya Bakshi
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - Keegan Walker
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - Chhabi K. Govind
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
| | - G. Rasul Chaudhry
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA; (C.M.); (C.B.); (S.B.); (K.W.); (C.K.G.)
- OU-WB Institute for Stem Cell and Regenerative Medicine, Rochester, MI 48309, USA
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19
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Mizi A, Zhang S, Papantonis A. Genome folding and refolding in differentiation and cellular senescence. Curr Opin Cell Biol 2020; 67:56-63. [PMID: 32911122 DOI: 10.1016/j.ceb.2020.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022]
Abstract
The spatial conformation of chromatin within the confines of eukaryotic cell nuclei is now acknowledged as a decisive epigenetic mechanism for the modulation of such cellular functions as gene expression regulation, DNA replication or DNA damage repair. Of course, these processes are tightly regulated during organismal development and markedly affected by cellular ageing. Thus, the question that arises is to what extent does folding or refolding of the genome in three-dimensional space underlie the progression of development or ageing? Herein, we discuss recent experimental and modelling evidence to address this question and revisit how these seemingly different processed might represent two sides of the same coin.
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Affiliation(s)
- Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Shu Zhang
- Institute of Pathology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075, Göttingen, Germany.
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20
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Lynch CJ, Bernad R, Calvo I, Serrano M. Manipulating the Mediator complex to induce naïve pluripotency. Exp Cell Res 2020; 395:112215. [PMID: 32771524 PMCID: PMC7584500 DOI: 10.1016/j.yexcr.2020.112215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/08/2020] [Accepted: 08/01/2020] [Indexed: 12/26/2022]
Abstract
Human naïve pluripotent stem cells (PSCs) represent an optimal homogenous starting point for molecular interventions and differentiation strategies. This is in contrast to the standard primed PSCs which fluctuate in identity and are transcriptionally heterogeneous. However, despite many efforts, the maintenance and expansion of human naïve PSCs remains a challenge. Here, we discuss our recent strategy for the stabilization of human PSC in the naïve state based on the use of a single chemical inhibitor of the related kinases CDK8 and CDK19. These kinases phosphorylate and negatively regulate the multiprotein Mediator complex, which is critical for enhancer-driven recruitment of RNA Pol II. The net effect of CDK8/19 inhibition is a global stimulation of enhancers, which in turn reinforces transcriptional programs including those related to cellular identity. In the case of pluripotent cells, the presence of CDK8/19i efficiently stabilizes the naïve state. Importantly, in contrast to previous chemical methods to induced the naïve state based on the inhibition of the FGF-MEK-ERK pathway, CDK8/19i-naïve human PSCs are chromosomally stable and retain developmental potential after long-term expansion. We suggest this could be related to the fact that CDK8/19 inhibition does not induce DNA demethylation. These principles may apply to other fate decisions.
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Affiliation(s)
- Cian J Lynch
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Raquel Bernad
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Isabel Calvo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain.
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21
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Somasundaram L, Levy S, Hussein AM, Ehnes DD, Mathieu J, Ruohola-Baker H. Epigenetic metabolites license stem cell states. Curr Top Dev Biol 2020; 138:209-240. [PMID: 32220298 DOI: 10.1016/bs.ctdb.2020.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
It has become clear during recent years that stem cells undergo metabolic remodeling during their activation process. While these metabolic switches take place in pluripotency as well as adult stem cell populations, the rules that govern the switch are not clear. In this review, we summarize some of the transitions in adult and pluripotent cell types and will propose that the key function in this process is the generation of epigenetic metabolites that govern critical epigenetic modifications, and therefore stem cell states.
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Affiliation(s)
- Logeshwaran Somasundaram
- Department of Biochemistry, University of Washington, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States
| | - Shiri Levy
- Department of Biochemistry, University of Washington, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States
| | - Abdiasis M Hussein
- Department of Biochemistry, University of Washington, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States
| | - Devon D Ehnes
- Department of Biochemistry, University of Washington, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States; Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, United States; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States.
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22
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Ehnes DD, Hussein AM, Ware CB, Mathieu J, Ruohola-Baker H. Combinatorial metabolism drives the naive to primed pluripotent chromatin landscape. Exp Cell Res 2020; 389:111913. [PMID: 32084392 DOI: 10.1016/j.yexcr.2020.111913] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/07/2020] [Accepted: 02/17/2020] [Indexed: 02/07/2023]
Abstract
Since epigenetic modifications are a key driver for cellular differentiation, the regulation of these modifications is tightly controlled. Interestingly, recent studies have revealed metabolic regulation for epigenetic modifications in pluripotent cells. As metabolic differences are prominent between naive (pre-implantation) and primed (post-implantation) pluripotent cells, the epigenetic changes regulated by metabolites has become an interesting topic of analysis. In this review we discuss how combinatorial metabolic activities drive the developmental progression through early pluripotent stages.
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Affiliation(s)
- D D Ehnes
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - A M Hussein
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - C B Ware
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Comparative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - J Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Comparative Medicine, University of Washington, Seattle, WA, 98109, USA.
| | - H Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA.
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23
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Goodwin J, Laslett AL, Rugg-Gunn PJ. The application of cell surface markers to demarcate distinct human pluripotent states. Exp Cell Res 2020; 387:111749. [PMID: 31790696 PMCID: PMC6983944 DOI: 10.1016/j.yexcr.2019.111749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 01/24/2023]
Abstract
Recent advances in human pluripotent stem cell (hPSC) research have uncovered different subpopulations within stem cell cultures and have captured a range of pluripotent states that hold distinct molecular and functional properties. At the two ends of the pluripotency spectrum are naïve and primed hPSC, whereby naïve hPSC grown in stringent conditions recapitulate features of the preimplantation human embryo, and the conventionally grown primed hPSC align closer to the early postimplantation embryo. Investigating these cell types will help to define the mechanisms that control early development and should provide new insights into stem cell properties such as cell identity, differentiation and reprogramming. Monitoring cell surface marker expression provides a valuable approach to resolve complex cell populations, to directly compare between cell types, and to isolate viable cells for functional experiments. This review discusses the discovery and applications of cell surface markers to study human pluripotent cell types with a particular focus on the transitions between naïve and primed states. Highlighted areas for future study include the potential functions for the identified cell surface proteins in pluripotency, the production of new high-quality monoclonal antibodies to naïve-specific protein epitopes and the use of cell surface markers to characterise subpopulations within pluripotent states.
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Affiliation(s)
- Jacob Goodwin
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Andrew L Laslett
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human. Sci Rep 2019; 9:17240. [PMID: 31754138 PMCID: PMC6872658 DOI: 10.1038/s41598-019-53681-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/25/2019] [Indexed: 11/08/2022] Open
Abstract
Recent progress has enabled the conversion of primed human embryonic stem cells (hESCs) to the naive state of pluripotency, resembling the well-characterized naive mouse ESCs (mESCs). However, a thorough histone epigenetic characterization of this conversion process is currently lacking, while its likeness to the mouse model has not been clearly established. Here, we profile the histone epigenome of hESCs during conversion in a time-resolved experimental design, using an untargeted mass spectrometry-based approach. In total, 23 histone post-translational modifications (hPTMs) changed significantly over time. H3K27Me3 was the most prominently increasing marker hPTM in naive hESCs. This is in line with previous reports in mouse, prompting us to compare all the shared hPTM fold changes between mouse and human, revealing a set of conserved hPTM markers for the naive state. Principally, we present the first roadmap of the changing human histone epigenome during the conversion of hESCs from the primed to the naive state. This further revealed similarities with mouse, which hint at a conserved mammalian epigenetic signature of the ground state of pluripotency.
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25
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Harvey A, Caretti G, Moresi V, Renzini A, Adamo S. Interplay between Metabolites and the Epigenome in Regulating Embryonic and Adult Stem Cell Potency and Maintenance. Stem Cell Reports 2019; 13:573-589. [PMID: 31597110 PMCID: PMC6830055 DOI: 10.1016/j.stemcr.2019.09.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/29/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022] Open
Abstract
The environment surrounding stem cells has the ability to elicit profound, heritable epigenetic changes orchestrated by multiple epigenetic mechanisms, which can be modulated by the level of specific metabolites. In this review, we highlight the significance of metabolism in regulating stem cell homeostasis, cell state, and differentiation capacity, using metabolic regulation of embryonic and adult muscle stem cells as examples, and cast light on the interaction between cellular metabolism and epigenetics. These new regulatory networks, based on the dynamic interplay between metabolism and epigenetics in stem cell biology, are important, not only for understanding tissue homeostasis, but to determine in vitro culture conditions which accurately support normal cell physiology.
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Affiliation(s)
- Alexandra Harvey
- School of BioSciences, University of Melbourne, Parkville, VIC 2010, Australia
| | - Giuseppina Caretti
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Viviana Moresi
- Department of Anatomy, Histology, Forensic Medicine & Orthopedics, Histology & Medical Embryology Section, Sapienza University of Rome and Interuniversity Institute of Myology, Rome, Italy.
| | - Alessandra Renzini
- Department of Anatomy, Histology, Forensic Medicine & Orthopedics, Histology & Medical Embryology Section, Sapienza University of Rome and Interuniversity Institute of Myology, Rome, Italy
| | - Sergio Adamo
- Department of Anatomy, Histology, Forensic Medicine & Orthopedics, Histology & Medical Embryology Section, Sapienza University of Rome and Interuniversity Institute of Myology, Rome, Italy
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