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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] [What about the content of this article? (0)] [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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Gelali E, Girelli G, Matsumoto M, Wernersson E, Custodio J, Mota A, Schweitzer M, Ferenc K, Li X, Mirzazadeh R, Agostini F, Schell JP, Lanner F, Crosetto N, Bienko M. iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture. Nat Commun 2019; 10:1636. [PMID: 30967549 PMCID: PMC6456570 DOI: 10.1038/s41467-019-09616-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/19/2019] [Indexed: 11/23/2022] Open
Abstract
DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface ( http://ifish4u.org ) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.
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Affiliation(s)
- Eleni Gelali
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Gabriele Girelli
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Masahiro Matsumoto
- R&D division, Medical Business Group, Sony Imaging Products & Solutions, Inc., Tokyo, 108-0075, Japan
| | - Erik Wernersson
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Joaquin Custodio
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Ana Mota
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Maud Schweitzer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Katalin Ferenc
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Xinge Li
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Reza Mirzazadeh
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - Federico Agostini
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden
| | - John P Schell
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, SE-171 77, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, SE-14186, Stockholm, Sweden
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, SE-171 77, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, SE-14186, Stockholm, Sweden
| | - Nicola Crosetto
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden.
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165, Stockholm, Sweden.
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Petropoulos S, Panula SP, Schell JP, Lanner F. Single-cell RNA sequencing: revealing human pre-implantation development, pluripotency and germline development. J Intern Med 2016; 280:252-64. [PMID: 27046137 DOI: 10.1111/joim.12493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Early human development is a dynamic, heterogeneous, complex and multidimensional process. During the first week, the single-cell zygote undergoes eight to nine rounds of cell division generating the multicellular blastocyst, which consists of hundreds of cells forming spatially organized embryonic and extra-embryonic tissues. At the level of transcription, degradation of maternal RNA commences at around the two-cell stage, coinciding with embryonic genome activation. Although numerous efforts have recently focused on delineating this process in humans, many questions still remain as thorough investigation has been limited by ethical issues, scarce availability of human embryos and the presence of minute amounts of DNA and RNA. In vitro cultures of embryonic stem cells provide some insight into early human development, but such studies have been confounded by analysis on a population level failing to appreciate cellular heterogeneity. Recent technical developments in single-cell RNA sequencing have provided a novel and powerful tool to explore the early human embryo in a systematic manner. In this review, we will discuss the advantages and disadvantages of the techniques utilized to specifically investigate human development and consider how the technology has yielded new insights into pre-implantation development, embryonic stem cells and the establishment of the germ line.
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Affiliation(s)
- S Petropoulos
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - S P Panula
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - J P Schell
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - F Lanner
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet and, Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
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Nazor KL, Boland MJ, Bibikova M, Klotzle B, Yu M, Glenn-Pratola VL, Schell JP, Coleman RL, Cabral-da-Silva MC, Schmidt U, Peterson SE, He C, Loring JF, Fan JB. Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells. Genomics 2014; 104:358-67. [PMID: 25179373 DOI: 10.1016/j.ygeno.2014.08.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/12/2014] [Accepted: 08/18/2014] [Indexed: 11/27/2022]
Abstract
5-hydroxymethylcytosine (5hmC), an oxidized derivative of 5-methylcytosine (5mC), has been implicated as an important epigenetic regulator of mammalian development. Current procedures use DNA sequencing methods to discriminate 5hmC from 5mC, limiting their accessibility to the scientific community. Here we report a method that combines TET-assisted bisulfite conversion with Illumina 450K DNA methylation arrays for a low-cost high-throughput approach that distinguishes 5hmC and 5mC signals at base resolution. Implementing this approach, termed "TAB-array", we assessed DNA methylation dynamics in the differentiation of human pluripotent stem cells into cardiovascular progenitors and neural precursor cells. With the ability to discriminate 5mC and 5hmC, we identified a large number of novel dynamically methylated genomic regions that are implicated in the development of these lineages. The increased resolution and accuracy afforded by this approach provides a powerful means to investigate the distinct contributions of 5mC and 5hmC in human development and disease.
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Affiliation(s)
- Kristopher L Nazor
- The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA
| | - Michael J Boland
- The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA
| | | | | | - Miao Yu
- The University of Chicago, Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, Chicago, IL 60637, USA
| | - Victoria L Glenn-Pratola
- The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA
| | - John P Schell
- The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA
| | - Ronald L Coleman
- The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA
| | | | | | - Suzanne E Peterson
- The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA
| | - Chuan He
- The University of Chicago, Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, Chicago, IL 60637, USA
| | - Jeanne F Loring
- The Scripps Research Institute, Department of Chemical Physiology, Center for Regenerative Medicine, La Jolla, CA 92037 USA.
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