1
|
Zhu M, Xu R, Yuan J, Wang J, Ren X, Cong T, You Y, Ju A, Xu L, Wang H, Zheng P, Tao H, Lin C, Yu H, Du J, Lin X, Xie W, Li Y, Lan X. Tracking-seq reveals the heterogeneity of off-target effects in CRISPR-Cas9-mediated genome editing. Nat Biotechnol 2024:10.1038/s41587-024-02307-y. [PMID: 38956324 DOI: 10.1038/s41587-024-02307-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 06/06/2024] [Indexed: 07/04/2024]
Abstract
The continued development of novel genome editors calls for a universal method to analyze their off-target effects. Here we describe a versatile method, called Tracking-seq, for in situ identification of off-target effects that is broadly applicable to common genome-editing tools, including Cas9, base editors and prime editors. Through tracking replication protein A (RPA)-bound single-stranded DNA followed by strand-specific library construction, Tracking-seq requires a low cell input and is suitable for in vitro, ex vivo and in vivo genome editing, providing a sensitive and practical genome-wide approach for off-target detection in various scenarios. We show, using the same guide RNA, that Tracking-seq detects heterogeneity in off-target effects between different editor modalities and between different cell types, underscoring the necessity of direct measurement in the original system.
Collapse
Affiliation(s)
- Ming Zhu
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China.
| | - Runda Xu
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China
| | - Junsong Yuan
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jiacheng Wang
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoyu Ren
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Tingting Cong
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yaxian You
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China
| | - Anji Ju
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China
| | - Longchen Xu
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Huimin Wang
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Peiyuan Zheng
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Huiying Tao
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- Department of Urology, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Chunhua Lin
- Department of Urology, Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Honghao Yu
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- Key Laboratory of Medical Biotechnology and Translational Medicine, Guilin Medical University, Guilin, China
| | - Juanjuan Du
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Xin Lin
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Wei Xie
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yinqing Li
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China.
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
| | - Xun Lan
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Tsinghua University, Beijing, China.
| |
Collapse
|
2
|
Fansler MM, Mitschka S, Mayr C. Quantifying 3'UTR length from scRNA-seq data reveals changes independent of gene expression. Nat Commun 2024; 15:4050. [PMID: 38744866 PMCID: PMC11094166 DOI: 10.1038/s41467-024-48254-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Although more than half of all genes generate transcripts that differ in 3'UTR length, current analysis pipelines only quantify the amount but not the length of mRNA transcripts. 3'UTR length is determined by 3' end cleavage sites (CS). We map CS in more than 200 primary human and mouse cell types and increase CS annotations relative to the GENCODE database by 40%. Approximately half of all CS are used in few cell types, revealing that most genes only have one or two major 3' ends. We incorporate the CS annotations into a computational pipeline, called scUTRquant, for rapid, accurate, and simultaneous quantification of gene and 3'UTR isoform expression from single-cell RNA sequencing (scRNA-seq) data. When applying scUTRquant to data from 474 cell types and 2134 perturbations, we discover extensive 3'UTR length changes across cell types that are as widespread and coordinately regulated as gene expression changes but affect mostly different genes. Our data indicate that mRNA abundance and mRNA length are two largely independent axes of gene regulation that together determine the amount and spatial organization of protein synthesis.
Collapse
Affiliation(s)
- Mervin M Fansler
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY, 10021, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sibylle Mitschka
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Christine Mayr
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY, 10021, USA.
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| |
Collapse
|
3
|
Waisman A, Sevlever F, Saulnier D, Francia M, Blanco R, Amín G, Lombardi A, Biani C, Palma MB, Scarafía A, Smucler J, La Greca A, Moro L, Sevlever G, Guberman A, Miriuka S. The transcription factor OCT6 promotes the dissolution of the naïve pluripotent state by repressing Nanog and activating a formative state gene regulatory network. Sci Rep 2024; 14:10420. [PMID: 38710730 PMCID: PMC11074312 DOI: 10.1038/s41598-024-59247-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
In the mouse embryo, the transition from the preimplantation to the postimplantation epiblast is governed by changes in the gene regulatory network (GRN) that lead to transcriptional, epigenetic, and functional changes. This transition can be faithfully recapitulated in vitro by the differentiation of mouse embryonic stem cells (mESCs) to epiblast-like cells (EpiLCs), that reside in naïve and formative states of pluripotency, respectively. However, the GRN that drives this conversion is not fully elucidated. Here we demonstrate that the transcription factor OCT6 is a key driver of this process. Firstly, we show that Oct6 is not expressed in mESCs but is rapidly induced as cells exit the naïve pluripotent state. By deleting Oct6 in mESCs, we find that knockout cells fail to acquire the typical morphological changes associated with the formative state when induced to differentiate. Additionally, the key naïve pluripotency TFs Nanog, Klf2, Nr5a2, Prdm14, and Esrrb were expressed at higher levels than in wild-type cells, indicating an incomplete dismantling of the naïve pluripotency GRN. Conversely, premature expression of Oct6 in naïve cells triggered a rapid morphological transformation mirroring differentiation, that was accompanied by the upregulation of the endogenous Oct6 as well as the formative genes Sox3, Zic2/3, Foxp1, Dnmt3A and FGF5. Strikingly, we found that OCT6 represses Nanog in a bistable manner and that this regulation is at the transcriptional level. Moreover, our findings also reveal that Oct6 is repressed by NANOG. Collectively, our results establish OCT6 as a key TF in the dissolution of the naïve pluripotent state and support a model where Oct6 and Nanog form a double negative feedback loop which could act as an important toggle mediating the transition to the formative state.
Collapse
Affiliation(s)
- Ariel Waisman
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina.
| | - Federico Sevlever
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Denisse Saulnier
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Marcos Francia
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Renata Blanco
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Guadalupe Amín
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Antonella Lombardi
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Celeste Biani
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - María Belén Palma
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Agustina Scarafía
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Joaquín Smucler
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Alejandro La Greca
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Lucía Moro
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Gustavo Sevlever
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Alejandra Guberman
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Santiago Miriuka
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina.
| |
Collapse
|
4
|
Lukauskas S, Tvardovskiy A, Nguyen NV, Stadler M, Faull P, Ravnsborg T, Özdemir Aygenli B, Dornauer S, Flynn H, Lindeboom RGH, Barth TK, Brockers K, Hauck SM, Vermeulen M, Snijders AP, Müller CL, DiMaggio PA, Jensen ON, Schneider R, Bartke T. Decoding chromatin states by proteomic profiling of nucleosome readers. Nature 2024; 627:671-679. [PMID: 38448585 PMCID: PMC10954555 DOI: 10.1038/s41586-024-07141-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
DNA and histone modifications combine into characteristic patterns that demarcate functional regions of the genome1,2. While many 'readers' of individual modifications have been described3-5, how chromatin states comprising composite modification signatures, histone variants and internucleosomal linker DNA are interpreted is a major open question. Here we use a multidimensional proteomics strategy to systematically examine the interaction of around 2,000 nuclear proteins with over 80 modified dinucleosomes representing promoter, enhancer and heterochromatin states. By deconvoluting complex nucleosome-binding profiles into networks of co-regulated proteins and distinct nucleosomal features driving protein recruitment or exclusion, we show comprehensively how chromatin states are decoded by chromatin readers. We find highly distinctive binding responses to different features, many factors that recognize multiple features, and that nucleosomal modifications and linker DNA operate largely independently in regulating protein binding to chromatin. Our online resource, the Modification Atlas of Regulation by Chromatin States (MARCS), provides in-depth analysis tools to engage with our results and advance the discovery of fundamental principles of genome regulation by chromatin states.
Collapse
Affiliation(s)
- Saulius Lukauskas
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Nhuong V Nguyen
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Mara Stadler
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig Maximilian University Munich, Munich, Germany
| | - Peter Faull
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Proteomic Sciences Technology Platform, The Francis Crick Institute, London, UK
- Northwestern Proteomics Core Facility, Northwestern University, Chicago, IL, USA
| | - Tina Ravnsborg
- VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Scarlett Dornauer
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Helen Flynn
- Proteomic Sciences Technology Platform, The Francis Crick Institute, London, UK
| | - Rik G H Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Teresa K Barth
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Munich, Germany
- Clinical Protein Analysis Unit (ClinZfP), Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Kevin Brockers
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Munich, Germany
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Christian L Müller
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig Maximilian University Munich, Munich, Germany
- Center for Computational Mathematics, Flatiron Institute, New York, NY, USA
| | - Peter A DiMaggio
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Ole N Jensen
- VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
- MRC Laboratory of Medical Sciences (LMS), London, UK.
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.
| |
Collapse
|
5
|
Li L, Ding X, Sheft AP, Schimenti JC. A high throughput CRISPR perturbation screen identifies epigenetic regulators impacting primordial germ cell development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582097. [PMID: 38463983 PMCID: PMC10925113 DOI: 10.1101/2024.02.26.582097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Certain environmental factors can impact fertility and reproductive parameters such as the number and quality of sperm and eggs. One possible mechanism is the perturbation of epigenetic landscapes in the germline. To explore this possibility, we conducted a CRISPRi screen of epigenetic-related genes to identify those that specifically perturb the differentiation of embryonic stem cells (ESCs) into primordial germ cell-like cells (PGCLCs), exploiting a highly scalable cytokine-free platform. Of the 701 genes screened, inhibition of 53 decreased the efficiency of PGCLC formation. NCOR2, a transcriptional repressor that acts via recruitment of Class I and Class IIa histone deacetylases (HDACs) to gene targets, was particularly potent in suppressing PGCLC differentiation. Consistent with evidence that histone deacetylation is crucial for germline differentiation, we found that the HDAC inhibitors (HDACi) valproic acid (VPA; an anti-convulsant) and sodium butyrate (SB; a widely-used dietary supplement) also suppressed ESC>PGCLC differentiation. Furthermore, exposure of developing mouse embryos to SB or VPA caused hypospermatogenesis. Transcriptome analyses of HDACi-treated, differentiating ESC>PGCLC cultures revealed suppression of germline-associated pathways and enhancement of somatic pathways. This work demonstrates the feasibility of conducting large-scale functional screens of genes, chemicals, or other agents that may impact germline development.
Collapse
|
6
|
Mu M, Li X, Dong L, Wang J, Cai Q, Hu Y, Wang D, Zhao P, Zhang L, Zhang D, Cheng S, Tan L, Wu F, Shi YG, Xu W, Shi Y, Shen H. METTL14 regulates chromatin bivalent domains in mouse embryonic stem cells. Cell Rep 2023; 42:112650. [PMID: 37314930 DOI: 10.1016/j.celrep.2023.112650] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 04/11/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
METTL14 (methyltransferase-like 14) is an RNA-binding protein that partners with METTL3 to mediate N6-methyladenosine (m6A) methylation. Recent studies identified a function for METTL3 in heterochromatin in mouse embryonic stem cells (mESCs), but the molecular function of METTL14 on chromatin in mESCs remains unclear. Here, we show that METTL14 specifically binds and regulates bivalent domains, which are marked by trimethylation of histone H3 lysine 27 (H3K27me3) and lysine 4 (H3K4me3). Knockout of Mettl14 results in decreased H3K27me3 but increased H3K4me3 levels, leading to increased transcription. We find that bivalent domain regulation by METTL14 is independent of METTL3 or m6A modification. METTL14 enhances H3K27me3 and reduces H3K4me3 by interacting with and probably recruiting the H3K27 methyltransferase polycomb repressive complex 2 (PRC2) and H3K4 demethylase KDM5B to chromatin. Our findings identify an METTL3-independent role of METTL14 in maintaining the integrity of bivalent domains in mESCs, thus indicating a mechanism of bivalent domain regulation in mammals.
Collapse
Affiliation(s)
- Mandi Mu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinze Li
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Dong
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jin Wang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qingqing Cai
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yajun Hu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Duanduan Wang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peng Zhao
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lei Zhang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Daixuan Zhang
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Siyi Cheng
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li Tan
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China
| | - Feizhen Wu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yujiang Geno Shi
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenqi Xu
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.
| | - Yang Shi
- Ludwig Institute for Cancer Research, Oxford Branch, Oxford University, Oxford, UK.
| | - Hongjie Shen
- Longevity and Aging Institute, the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.
| |
Collapse
|
7
|
Sullivan AE. Epigenetic Control of Cell Potency and Fate Determination during Mammalian Gastrulation. Genes (Basel) 2023; 14:1143. [PMID: 37372324 DOI: 10.3390/genes14061143] [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: 04/21/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Pluripotent embryonic stem cells have a unique and characteristic epigenetic profile, which is critical for differentiation to all embryonic germ lineages. When stem cells exit the pluripotent state and commit to lineage-specific identities during the process of gastrulation in early embryogenesis, extensive epigenetic remodelling mediates both the switch in cellular programme and the loss of potential to adopt alternative lineage programmes. However, it remains to be understood how the stem cell epigenetic profile encodes pluripotency, or how dynamic epigenetic regulation helps to direct cell fate specification. Recent advances in stem cell culture techniques, cellular reprogramming, and single-cell technologies that can quantitatively profile epigenetic marks have led to significant insights into these questions, which are important for understanding both embryonic development and cell fate engineering. This review provides an overview of key concepts and highlights exciting new advances in the field.
Collapse
Affiliation(s)
- Adrienne E Sullivan
- Quantitative Stem Cell Biology Lab, Francis Crick Institute, London NW1 1AT, UK
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5000, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5000, Australia
| |
Collapse
|
8
|
Xie G, Lee JE, Senft AD, Park YK, Jang Y, Chakraborty S, Thompson JJ, McKernan K, Liu C, Macfarlan TS, Rocha PP, Peng W, Ge K. MLL3/MLL4 methyltransferase activities control early embryonic development and embryonic stem cell differentiation in a lineage-selective manner. Nat Genet 2023; 55:693-705. [PMID: 37012455 DOI: 10.1038/s41588-023-01356-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/27/2023] [Indexed: 04/05/2023]
Abstract
H3K4me1 methyltransferases MLL3 (KMT2C) and MLL4 (KMT2D) are critical for enhancer activation, cell differentiation and development. However, roles of MLL3/4 enzymatic activities and MLL3/4-mediated enhancer H3K4me1 in these processes remain unclear. Here we report that constitutive elimination of both MLL3 and MLL4 enzymatic activities prevents initiation of gastrulation and leads to early embryonic lethality in mice. However, selective elimination of MLL3/4 enzymatic activities in embryonic, but not extraembryonic, lineages leaves gastrulation largely intact. Consistent with this, embryonic stem cells (ESCs) lacking MLL3/4 enzymatic activities can differentiate toward the three embryonic germ layers but show aberrant differentiation to extraembryonic endoderm (ExEn) and trophectoderm. The failure in ExEn differentiation can be attributed to markedly reduced enhancer-binding of the lineage-determining transcription factor GATA6. Furthermore, we show that MLL3/4-catalyzed H3K4me1 is largely dispensable for enhancer activation during ESC differentiation. Together, our findings suggest a lineage-selective, but enhancer activation-independent, role of MLL3/4 methyltransferase activities in early embryonic development and ESC differentiation.
Collapse
Affiliation(s)
- Guojia Xie
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ji-Eun Lee
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anna D Senft
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Young-Kwon Park
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Younghoon Jang
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shreeta Chakraborty
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Joyce J Thompson
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kaitlin McKernan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Weiqun Peng
- Departments of Physics and Anatomy and Cell Biology, The George Washington University, Washington, DC, USA
| | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
9
|
Boileau RM, Chen KX, Blelloch R. Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation. Genome Biol 2023; 24:41. [PMID: 36869380 PMCID: PMC9983171 DOI: 10.1186/s13059-023-02883-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/19/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Enhancers are essential in defining cell fates through the control of cell-type-specific gene expression. Enhancer activation is a multi-step process involving chromatin remodelers and histone modifiers including the monomethylation of H3K4 (H3K4me1) by MLL3 (KMT2C) and MLL4 (KMT2D). MLL3/4 are thought to be critical for enhancer activation and cognate gene expression including through the recruitment of acetyltransferases for H3K27. RESULTS Here we test this model by evaluating the impact of MLL3/4 loss on chromatin and transcription during early differentiation of mouse embryonic stem cells. We find that MLL3/4 activity is required at most if not all sites that gain or lose H3K4me1 but is largely dispensable at sites that remain stably methylated during this transition. This requirement extends to H3K27 acetylation (H3K27ac) at most transitional sites. However, many sites gain H3K27ac independent of MLL3/4 or H3K4me1 including enhancers regulating key factors in early differentiation. Furthermore, despite the failure to gain active histone marks at thousands of enhancers, transcriptional activation of nearby genes is largely unaffected, thus uncoupling the regulation of these chromatin events from transcriptional changes during this transition. These data challenge current models of enhancer activation and imply distinct mechanisms between stable and dynamically changing enhancers. CONCLUSIONS Collectively, our study highlights gaps in knowledge about the steps and epistatic relationships of enzymes necessary for enhancer activation and cognate gene transcription.
Collapse
Affiliation(s)
- Ryan M. Boileau
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, USA
- Developmental and Stem Cell Biology Graduate Program , University of California San Francisco, San Francisco, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA USA
| | - Kevin X. Chen
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, USA
- Developmental and Stem Cell Biology Graduate Program , University of California San Francisco, San Francisco, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA USA
| |
Collapse
|
10
|
Chiu FY, Kvadas RM, Mheidly Z, Shahbandi A, Jackson JG. Could senescence phenotypes strike the balance to promote tumor dormancy? Cancer Metastasis Rev 2023; 42:143-160. [PMID: 36735097 DOI: 10.1007/s10555-023-10089-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023]
Abstract
After treatment and surgery, patient tumors can initially respond followed by a rapid relapse, or respond well and seemingly be cured, but then recur years or decades later. The state of surviving cancer cells during the long, undetected period is termed dormancy. By definition, the dormant tumor cells do not proliferate to create a mass that is detectable or symptomatic, but also never die. An intrinsic state and microenvironment that are inhospitable to the tumor would bias toward cell death and complete eradication, while conditions that favor the tumor would enable growth and relapse. In neither case would clinical dormancy be observed. Normal cells and tumor cells can enter a state of cellular senescence after stress such as that caused by cancer therapy. Senescence is characterized by a stable cell cycle arrest mediated by chromatin modifications that cause gene expression changes and a secretory phenotype involving many cytokines and chemokines. Senescent cell phenotypes have been shown to be both tumor promoting and tumor suppressive. The balance of these opposing forces presents an attractive model to explain tumor dormancy: phenotypes of stable arrest and immune suppression could promote survival, while reversible epigenetic programs combined with cytokines and growth factors that promote angiogenesis, survival, and proliferation could initiate the emergence from dormancy. In this review, we examine the phenotypes that have been characterized in different normal and cancer cells made senescent by various stresses and how these might explain the characteristics of tumor dormancy.
Collapse
Affiliation(s)
- Fang-Yen Chiu
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Raegan M Kvadas
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Zeinab Mheidly
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
| | - Ashkan Shahbandi
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA
| | - James G Jackson
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, 1430 Tulane Avenue, New Orleans, LA, 70112, USA.
| |
Collapse
|
11
|
Luo Q, Pui HP, Chen J, Yu L, Jannig PR, Pei Y, Zhao L, Chen X, Petropoulos S, Ruas JL, Wu J, Deng Q. Epiblast-like stem cells established by Wnt/β-catenin signaling manifest distinct features of formative pluripotency and germline competence. Cell Rep 2023; 42:112021. [PMID: 36848234 PMCID: PMC10026833 DOI: 10.1016/j.celrep.2023.112021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/05/2022] [Accepted: 01/06/2023] [Indexed: 01/25/2023] Open
Abstract
Different formative pluripotent stem cells harboring similar functional properties have been recently established to be lineage neutral and germline competent yet have distinct molecular identities. Here, we show that WNT/β-catenin signaling activation sustains transient mouse epiblast-like cells as epiblast-like stem cells (EpiLSCs). EpiLSCs display metastable formative pluripotency with bivalent cellular energy metabolism and unique transcriptomic features and chromatin accessibility. We develop single-cell stage label transfer (scSTALT) to study the formative pluripotency continuum and reveal that EpiLSCs recapitulate a unique developmental period in vivo, filling the gap of the formative pluripotency continuum between other published formative stem cells. WNT/β-catenin signaling activation counteracts differentiation effects of activin A and bFGF by preventing complete dissolution of naive pluripotency regulatory network. Moreover, EpiLSCs have direct competence toward germline specification, which is further matured by an FGF receptor inhibitor. Our EpiLSCs can serve as an in vitro model for mimicking and studying early post-implantation development and pluripotency transition.
Collapse
Affiliation(s)
- Qing Luo
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Han-Pin Pui
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden; Center for Molecular Medicine, Karolinska University Hospital, 171 77 Stockholm, Sweden; Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, 141 52 Huddinge, Sweden
| | - Jiayu Chen
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 20092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 20092, China
| | - Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paulo R Jannig
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Yu Pei
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden; Center for Molecular Medicine, Karolinska University Hospital, 171 77 Stockholm, Sweden
| | - Linxuan Zhao
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Sophie Petropoulos
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, 141 52 Huddinge, Sweden; Department of Medicine, Centre de recherche du CHUM, University of Montreal, Montreal, QC H2X 0A9, Canada
| | - Jorge L Ruas
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qiaolin Deng
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden; Center for Molecular Medicine, Karolinska University Hospital, 171 77 Stockholm, Sweden.
| |
Collapse
|
12
|
Developmental phenomics suggests that H3K4 monomethylation confers multi-level phenotypic robustness. Cell Rep 2022; 41:111832. [PMID: 36516782 PMCID: PMC9764455 DOI: 10.1016/j.celrep.2022.111832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/29/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
How histone modifications affect animal development remains difficult to ascertain. Despite the prevalence of histone 3 lysine 4 monomethylation (H3K4me1) on enhancers, hypomethylation appears to have minor effects on phenotype and viability. Here, we genetically reduce H3K4me1 deposition in Drosophila melanogaster and find that hypomethylation reduces transcription factor enrichment in nuclear microenvironments, disrupts gene expression, and reduces phenotypic robustness. Using a developmental phenomics approach, we find changes in morphology, metabolism, behavior, and offspring production. However, many phenotypic changes are only detected when hypomethylated flies develop outside of standard laboratory environments or with specific genetic backgrounds. Therefore, quantitative phenomics measurements can unravel how pleiotropic modulators of gene expression affect developmental robustness under conditions resembling the natural environments of a species.
Collapse
|
13
|
Ramakrishna NB, Battistoni G, Surani MA, Hannon GJ, Miska EA. Mouse primordial germ-cell-like cells lack piRNAs. Dev Cell 2022; 57:2661-2668.e5. [PMID: 36473462 DOI: 10.1016/j.devcel.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/03/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are small RNAs bound by PIWI-clade Argonaute proteins that function to silence transposable elements (TEs). Following mouse primordial germ cell (mPGC) specification around E6.25, fetal piRNAs emerge in male gonocytes from E13.5 onward. The in vitro differentiation of mPGC-like cells (mPGCLCs) has raised the possibility of studying the fetal piRNA pathway in greater depth. However, using single-cell RNA-seq and RT-qPCR along mPGCLC differentiation, we find that piRNA pathway factors are not fully expressed in Day 6 mPGCLCs. Moreover, we do not detect piRNAs across a panel of Day 6 mPGCLC lines using small RNA-seq. Our combined efforts highlight that in vitro differentiated Day 6 mPGCLCs do not yet resemble E13.5 or later mouse gonocytes where the piRNA pathway is active. This Matters Arising paper is in response to von Meyenn et al. (2016), published in Developmental Cell. See also the correction by von Meyenn et al. published in this issue.
Collapse
Affiliation(s)
- Navin B Ramakrishna
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK
| | - Giorgia Battistoni
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - M Azim Surani
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK; Wellcome/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Gregory J Hannon
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK.
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
| |
Collapse
|
14
|
Millán-Zambrano G, Burton A, Bannister AJ, Schneider R. Histone post-translational modifications - cause and consequence of genome function. Nat Rev Genet 2022; 23:563-580. [PMID: 35338361 DOI: 10.1038/s41576-022-00468-7] [Citation(s) in RCA: 268] [Impact Index Per Article: 134.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2022] [Indexed: 12/16/2022]
Abstract
Much has been learned since the early 1960s about histone post-translational modifications (PTMs) and how they affect DNA-templated processes at the molecular level. This understanding has been bolstered in the past decade by the identification of new types of histone PTM, the advent of new genome-wide mapping approaches and methods to deposit or remove PTMs in a locally and temporally controlled manner. Now, with the availability of vast amounts of data across various biological systems, the functional role of PTMs in important processes (such as transcription, recombination, replication, DNA repair and the modulation of genomic architecture) is slowly emerging. This Review explores the contribution of histone PTMs to the regulation of genome function by discussing when these modifications play a causative (or instructive) role in DNA-templated processes and when they are deposited as a consequence of such processes, to reinforce and record the event. Important advances in the field showing that histone PTMs can exert both direct and indirect effects on genome function are also presented.
Collapse
Affiliation(s)
- Gonzalo Millán-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Adam Burton
- Institute of Epigenetics and Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Andrew J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Center Munich, Munich, Germany.
- Faculty of Biology, Ludwig Maximilian University (LMU) of Munich, Munich, Germany.
| |
Collapse
|
15
|
UvKmt2-Mediated H3K4 Trimethylation Is Required for Pathogenicity and Stress Response in Ustilaginoidea virens. J Fungi (Basel) 2022; 8:jof8060553. [PMID: 35736036 PMCID: PMC9225167 DOI: 10.3390/jof8060553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic modification is important for cellular functions. Trimethylation of histone H3 lysine 4 (H3K4me3), which associates with transcriptional activation, is one of the important epigenetic modifications. In this study, the biological functions of UvKmt2-mediated H3K4me3 modification were characterized in Ustilaginoidea virens, which is the causal agent of the false smut disease, one of the most destructive diseases in rice. Phenotypic analyses of the ΔUvkmt2 mutant revealed that UvKMT2 is necessary for growth, conidiation, secondary spore formation, and virulence in U. virens. Immunoblotting and chromatin immunoprecipitation assay followed by sequencing (ChIP-seq) showed that UvKMT2 is required for the establishment of H3K4me3, which covers 1729 genes of the genome in U. virens. Further RNA-seq analysis demonstrated that UvKmt2-mediated H3K4me3 acts as an important role in transcriptional activation. In particular, H3K4me3 modification involves in the transcriptional regulation of conidiation-related and pathogenic genes, including two important mitogen-activated protein kinases UvHOG1 and UvPMK1. The down-regulation of UvHOG1 and UvPMK1 genes may be one of the main reasons for the reduced pathogenicity and stresses adaptability of the ∆Uvkmt2 mutant. Overall, H3K4me3, established by histone methyltransferase UvKMT2, contributes to fungal development, secondary spore formation, virulence, and various stress responses through transcriptional regulation in U. virens.
Collapse
|
16
|
Quan Y, Wang M, Xu C, Wang X, Wu Y, Qin D, Lin Y, Lu X, Lu F, Li L. Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition. Nucleic Acids Res 2022; 50:4414-4435. [PMID: 35390160 PMCID: PMC9071485 DOI: 10.1093/nar/gkac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 03/11/2022] [Accepted: 03/26/2022] [Indexed: 11/14/2022] Open
Abstract
Mammalian early epiblasts at different phases are characterized by naïve, formative, and primed pluripotency states, involving extensive transcriptome changes. Here, we report that deadenylase Cnot8 of Ccr4-Not complex plays essential roles during the transition from naïve to formative state. Knock out (KO) Cnot8 resulted in early embryonic lethality in mice, but Cnot8 KO embryonic stem cells (ESCs) could be established. Compared with the cells differentiated from normal ESCs, Cnot8 KO cells highly expressed a great many genes during their differentiation into the formative state, including several hundred naïve-like genes enriched in lipid metabolic process and gene expression regulation that may form the naïve regulation networks. Knockdown expression of the selected genes of naïve regulation networks partially rescued the differentiation defects of Cnot8 KO ESCs. Cnot8 depletion led to the deadenylation defects of its targets, increasing their poly(A) tail lengths and half-life, eventually elevating their expression levels. We further found that Cnot8 was involved in the clearance of targets through its deadenylase activity and the binding of Ccr4-Not complex, as well as the interacting with Tob1 and Pabpc1. Our results suggest that Cnot8 eliminates naïve regulation networks through mRNA clearance, and is essential for naïve-to-formative pluripotency transition.
Collapse
Affiliation(s)
- Yujun Quan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meijiao Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengpeng Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxuan Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xukun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
17
|
Aljahani A, Hua P, Karpinska MA, Quililan K, Davies JOJ, Oudelaar AM. Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Nat Commun 2022; 13:2139. [PMID: 35440598 PMCID: PMC9019034 DOI: 10.1038/s41467-022-29696-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Enhancers and promoters predominantly interact within large-scale topologically associating domains (TADs), which are formed by loop extrusion mediated by cohesin and CTCF. However, it is unclear whether complex chromatin structures exist at sub-kilobase-scale and to what extent fine-scale regulatory interactions depend on loop extrusion. To address these questions, we present an MNase-based chromosome conformation capture (3C) approach, which has enabled us to generate the most detailed local interaction data to date (20 bp resolution) and precisely investigate the effects of cohesin and CTCF depletion on chromatin architecture. Our data reveal that cis-regulatory elements have distinct internal nano-scale structures, within which local insulation is dependent on CTCF, but which are independent of cohesin. In contrast, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression.
Collapse
Affiliation(s)
- Abrar Aljahani
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Peng Hua
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | | | - Kimberly Quililan
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - A Marieke Oudelaar
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| |
Collapse
|
18
|
Gjaltema RAF, Schwämmle T, Kautz P, Robson M, Schöpflin R, Ravid Lustig L, Brandenburg L, Dunkel I, Vechiatto C, Ntini E, Mutzel V, Schmiedel V, Marsico A, Mundlos S, Schulz EG. Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus. Mol Cell 2022; 82:190-208.e17. [PMID: 34932975 DOI: 10.1016/j.molcel.2021.11.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
Developmental genes such as Xist, which initiates X chromosome inactivation, are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatiotemporal expression patterns. Xist integrates information on X chromosome dosage and developmental stage to trigger X inactivation in the epiblast specifically in female embryos. Through a pooled CRISPR screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist at the onset of random X inactivation. Chromatin profiling reveals that X-dosage controls the promoter-proximal region, while differentiation cues activate several distal enhancers. The strongest distal element lies in an enhancer cluster associated with a previously unannotated Xist-enhancing regulatory transcript, which we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. With this study, we start to disentangle how multiple, functionally distinct regulatory elements interact to generate complex expression patterns in mammals.
Collapse
Affiliation(s)
- Rutger A F Gjaltema
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Till Schwämmle
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Pauline Kautz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Michael Robson
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, Edinburgh, UK
| | - Robert Schöpflin
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Liat Ravid Lustig
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lennart Brandenburg
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ilona Dunkel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Carolina Vechiatto
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Evgenia Ntini
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Verena Mutzel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Vera Schmiedel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center München, 85764 Neuherberg, Germany
| | - Stefan Mundlos
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| |
Collapse
|