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Leo L, Colonna Romano N. Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease. Int J Mol Sci 2021; 22:ijms22168809. [PMID: 34445507 PMCID: PMC8395756 DOI: 10.3390/ijms22168809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic regulators play a crucial role in establishing and maintaining gene expression states. To date, the main efforts to study cellular heterogeneity have focused on elucidating the variable nature of the chromatin landscape. Specific chromatin organisation is fundamental for normal organogenesis and developmental homeostasis and can be affected by different environmental factors. The latter can lead to detrimental alterations in gene transcription, as well as pathological conditions such as cancer. Epigenetic marks regulate the transcriptional output of cells. Centromeres are chromosome structures that are epigenetically regulated and are crucial for accurate segregation. The advent of single-cell epigenetic profiling has provided finer analytical resolution, exposing the intrinsic peculiarities of different cells within an apparently homogenous population. In this review, we discuss recent advances in methodologies applied to epigenetics, such as CUT&RUN and CUT&TAG. Then, we compare standard and emerging single-cell techniques and their relevance for investigating human diseases. Finally, we describe emerging methodologies that investigate centromeric chromatin specification and neocentromere formation.
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Affiliation(s)
- Adam Burton
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377, München, Germany. .,Faculty of Biology, Ludwig-Maximilians Universität, München, Germany.
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53
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Rachez C, Legendre R, Costallat M, Varet H, Yi J, Kornobis E, Muchardt C. HP1γ binding pre-mRNA intronic repeats modulates RNA splicing decisions. EMBO Rep 2021; 22:e52320. [PMID: 34312949 DOI: 10.15252/embr.202052320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 12/30/2022] Open
Abstract
HP1 proteins are best known as markers of heterochromatin and gene silencing. Yet, they are also RNA-binding proteins and the HP1γ/CBX3 family member is present on transcribed genes together with RNA polymerase II, where it regulates co-transcriptional processes such as alternative splicing. To gain insight in the role of the RNA-binding activity of HP1γ in transcriptionally active chromatin, we have captured and analysed RNAs associated with this protein. We find that HP1γ is specifically targeted to hexameric RNA motifs and coincidentally transposable elements of the SINE family. As these elements are abundant in introns, while essentially absent from exons, the HP1γ RNA association tethers unspliced pre-mRNA to chromatin via the intronic regions and limits the usage of intronic cryptic splice sites. Thus, our data unveil novel determinants in the relationship between chromatin and co-transcriptional splicing.
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Affiliation(s)
- Christophe Rachez
- Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France.,CNRS UMR 8256, Biological Adaptation and Aging, Paris, France.,Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Rachel Legendre
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France.,Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Mickaël Costallat
- Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France.,CNRS UMR 8256, Biological Adaptation and Aging, Paris, France.,Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Hugo Varet
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France.,Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Jia Yi
- Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France.,Sorbonne Université, Ecole Doctorale Complexité du Vivant (ED515), Paris, France
| | - Etienne Kornobis
- Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
| | - Christian Muchardt
- Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France.,CNRS UMR 8256, Biological Adaptation and Aging, Paris, France.,Epigenetic Regulation Unit, Institut Pasteur, CNRS UMR 3738, Paris, France
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54
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Hsu CL, Chong SY, Lin CY, Kao CF. Histone dynamics during DNA replication stress. J Biomed Sci 2021; 28:48. [PMID: 34144707 PMCID: PMC8214274 DOI: 10.1186/s12929-021-00743-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/08/2021] [Indexed: 01/20/2023] Open
Abstract
Accurate and complete replication of the genome is essential not only for genome stability but also for cell viability. However, cells face constant threats to the replication process, such as spontaneous DNA modifications and DNA lesions from endogenous and external sources. Any obstacle that slows down replication forks or perturbs replication dynamics is generally considered to be a form of replication stress, and the past decade has seen numerous advances in our understanding of how cells respond to and resolve such challenges. Furthermore, recent studies have also uncovered links between defects in replication stress responses and genome instability or various diseases, such as cancer. Because replication stress takes place in the context of chromatin, histone dynamics play key roles in modulating fork progression and replication stress responses. Here, we summarize the current understanding of histone dynamics in replication stress, highlighting recent advances in the characterization of fork-protective mechanisms.
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Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Shin Yen Chong
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Yeh Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan.
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55
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Programmed suppression of oxidative phosphorylation and mitochondrial function by gestational alcohol exposure correlate with widespread increases in H3K9me2 that do not suppress transcription. Epigenetics Chromatin 2021; 14:27. [PMID: 34130715 PMCID: PMC8207718 DOI: 10.1186/s13072-021-00403-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/08/2021] [Indexed: 12/15/2022] Open
Abstract
Background A critical question emerging in the field of developmental toxicology is whether alterations in chromatin structure induced by toxicant exposure control patterns of gene expression or, instead, are structural changes that are part of a nuclear stress response. Previously, we used a mouse model to conduct a three-way comparison between control offspring, alcohol-exposed but phenotypically normal animals, and alcohol-exposed offspring exhibiting craniofacial and central nervous system structural defects. In the cerebral cortex of animals exhibiting alcohol-induced dysgenesis, we identified a dramatic increase in the enrichment of dimethylated histone H3, lysine 9 (H3K9me2) within the regulatory regions of key developmental factors driving histogenesis in the brain. However, whether this change in chromatin structure is causally involved in the development of structural defects remains unknown. Results Deep-sequencing analysis of the cortex transcriptome reveals that the emergence of alcohol-induced structural defects correlates with disruptions in the genetic pathways controlling oxidative phosphorylation and mitochondrial function. The majority of the affected pathways are downstream targets of the mammalian target of rapamycin complex 2 (mTORC2), indicating that this stress-responsive complex plays a role in propagating the epigenetic memory of alcohol exposure through gestation. Importantly, transcriptional disruptions of the pathways regulating oxidative homeostasis correlate with the emergence of increased H3K9me2 across genic, repetitive, and non-transcribed regions of the genome. However, although associated with gene silencing, none of the candidate genes displaying increased H3K9me2 become transcriptionally repressed, nor do they exhibit increased markers of canonical heterochromatin. Similar to studies in C. elegans, disruptions in oxidative homeostasis induce the chromatin looping factor SATB2, but in mammals, this protein does not appear to drive increased H3K9me2 or altered patterns of gene expression. Conclusions Our studies demonstrate that changes in H3K9me2 associate with alcohol-induced congenital defects, but that this epigenetic change does not correlate with transcriptional suppression. We speculate that the mobilization of SATB2 and increased enrichment of H3K9me2 may be components of a nuclear stress response that preserve chromatin integrity and interactions under prolonged oxidative stress. Further, we postulate that while this response may stabilize chromatin structure, it compromises the nuclear plasticity required for normal differentiation. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00403-w.
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Vodnala M, Choi EB, Fong YW. Low complexity domains, condensates, and stem cell pluripotency. World J Stem Cells 2021; 13:416-438. [PMID: 34136073 PMCID: PMC8176841 DOI: 10.4252/wjsc.v13.i5.416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Biological reactions require self-assembly of factors in the complex cellular milieu. Recent evidence indicates that intrinsically disordered, low-complexity sequence domains (LCDs) found in regulatory factors mediate diverse cellular processes from gene expression to DNA repair to signal transduction, by enriching specific biomolecules in membraneless compartments or hubs that may undergo liquid-liquid phase separation (LLPS). In this review, we discuss how embryonic stem cells take advantage of LCD-driven interactions to promote cell-specific transcription, DNA damage response, and DNA repair. We propose that LCD-mediated interactions play key roles in stem cell maintenance and safeguarding genome integrity.
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Affiliation(s)
- Munender Vodnala
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Eun-Bee Choi
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Yick W Fong
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
- Harvard Stem Cell Institute, Cambridge, MA 02138, United States.
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57
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Su Z, Liu G, Zhang B, Lin Z, Huang D. Natural Antisense Transcript PEBP1P3 Regulates the RNA Expression, DNA Methylation and Histone Modification of CD45 Gene. Genes (Basel) 2021; 12:genes12050759. [PMID: 34067766 PMCID: PMC8156488 DOI: 10.3390/genes12050759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/15/2021] [Indexed: 02/05/2023] Open
Abstract
The leukocyte common antigen CD45 is a transmembrane phosphatase expressed on all nucleated hemopoietic cells, and the expression levels of its splicing isoforms are closely related to the development and function of lymphocytes. PEBP1P3 is a natural antisense transcript from the opposite strand of CD45 intron 2 and is predicted to be a noncoding RNA. The genotype-tissue expression and quantitative PCR data suggested that PEBP1P3 might be involved in the regulation of expression of CD45 splicing isoforms. To explore the regulatory mechanism of PEBP1P3 in CD45 expression, DNA methylation and histone modification were detected by bisulfate sequencing PCR and chromatin immunoprecipitation assays, respectively. The results showed that after the antisense RNA PEBP1P3 was knocked down by RNA interference, the DNA methylation of CD45 intron 2 was decreased and histone H3K9 and H3K36 trimethylation at the alternative splicing exons of CD45 DNA was increased. Knockdown of PEBP1P3 also increased the binding levels of chromatin conformation organizer CTCF at intron 2 and the alternative splicing exons of CD45. The present results indicate that the natural antisense RNA PEBP1P3 regulated the alternative splicing of CD45 RNA, and that might be correlated with the regulation of histone modification and DNA methylation.
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Affiliation(s)
- Zhongjing Su
- Department of Histology and Embryology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China;
- Correspondence: (Z.S.); (D.H.)
| | - Guangyu Liu
- Department of Cell Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China;
| | - Bin Zhang
- Department of Histology and Embryology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China;
| | - Ze Lin
- Department of Central Laboratory, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China;
| | - Dongyang Huang
- Department of Cell Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China;
- Correspondence: (Z.S.); (D.H.)
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58
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Yoder KE, Rabe AJ, Fishel R, Larue RC. Strategies for Targeting Retroviral Integration for Safer Gene Therapy: Advances and Challenges. Front Mol Biosci 2021; 8:662331. [PMID: 34055882 PMCID: PMC8149907 DOI: 10.3389/fmolb.2021.662331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Retroviruses are obligate intracellular parasites that must integrate a copy of the viral genome into the host DNA. The integration reaction is performed by the viral enzyme integrase in complex with the two ends of the viral cDNA genome and yields an integrated provirus. Retroviral vector particles are attractive gene therapy delivery tools due to their stable integration. However, some retroviral integration events may dysregulate host oncogenes leading to cancer in gene therapy patients. Multiple strategies to target retroviral integration, particularly to genetic safe harbors, have been tested with limited success. Attempts to target integration may be limited by the multimerization of integrase or the presence of host co-factors for integration. Several retroviral integration complexes have evolved a mechanism of tethering to chromatin via a host protein. Integration host co-factors bind chromatin, anchoring the complex and allowing integration. The tethering factor allows for both close proximity to the target DNA and specificity of targeting. Each retrovirus appears to have distinct preferences for DNA sequence and chromatin features at the integration site. Tethering factors determine the preference for chromatin features, but do not affect the subtle sequence preference at the integration site. The sequence preference is likely intrinsic to the integrase protein. New developments may uncouple the requirement for a tethering factor and increase the ability to redirect retroviral integration.
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Affiliation(s)
- Kristine E Yoder
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Anthony J Rabe
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Richard Fishel
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Ross C Larue
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
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59
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Ren K, Mou YN, Tong SM, Ying SH, Feng MG. DIM5/KMT1 controls fungal insect pathogenicity and genome stability by methylation of histone H3K4, H3K9 and H3K36. Virulence 2021; 12:1306-1322. [PMID: 33955325 PMCID: PMC8115510 DOI: 10.1080/21505594.2021.1923232] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mono-, di- and tri-methylation of histone H3 Lys 9, Lys 4, and Lys 36 (H3K_me1/me2/me3) required for mediation of DNA-based cellular events in eukaryotes usually rely upon the activities of histone lysine methyltransferases (KMTs) classified to the KMT1, KMT2, and KMT3 families, respectively. Here, an H3K9-specific DIM5/KMT1 orthologue, which lacks a C-terminal post-SET domain and localizes mainly in nucleus, is reported to have both conserved and noncanonical roles in methylating the H3 core lysines in Beauveria bassiana, an insect-pathogenic fungus serving as a main source of wide-spectrum fungal insecticides. Disruption of dim5 led to abolishment of H3K9me3 and marked attenuation of H3K4me1/me2, H3K9me1/me2 and H3K36me2. Consequently, the Δdim5 mutant lost the whole insect pathogenicity through normal cuticle infection, and was compromised severely in virulence through cuticle-bypassing infection (hemocoel injection) and also in a series of cellular events critical for the fungal virulence and lifecycle in vivo and in vitro, including reduced hyphal growth, blocked conidiation, impeded proliferation in vivo, altered carbohydrate epitopes, disturbed cell cycle, reduced biosynthesis and secretion of cuticle-degrading enzymes, and increased sensitivities to various stresses. Among 1,201 dysregulated genes (up/down ratio: 712:489) associated with those phenotypic changes, 92 (up/down ratio: 59:33) encode transcription factors and proteins or enzymes involved in posttranslational modifications, implying that the DIM5-methylated H3 core lysines could act as preferential marks of those transcription-active genes crucial for global gene regulation. These findings uncover a novel scenario of DIM5 and its indispensability for insect-pathogenic lifestyle and genome stability of B. bassiana.
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Affiliation(s)
- Kang Ren
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ya-Ni Mou
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sen-Miao Tong
- College of Agricultural and Food Science, Zhejiang A & F University, Lin'an, Zhejiang, China
| | - Sheng-Hua Ying
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ming-Guang Feng
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
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Ding X, Zhang A, Li C, Ma L, Tang S, Wang Q, Yang G, Li J. The role of H3K9me2-regulated base excision repair genes in the repair of DNA damage induced by arsenic in HaCaT cells and the effects of Ginkgo biloba extract intervention. ENVIRONMENTAL TOXICOLOGY 2021; 36:850-860. [PMID: 33378118 DOI: 10.1002/tox.23088] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Arsenic is an established human carcinogen that can induce DNA damage; however, the precise mechanism remains unknown. Histone modification is of great significance in chemical toxicity and carcinogenesis. To investigate the role of histone H3K9me2 in arsenic-induced DNA damage, HaCaT cells were exposed to sodium arsenite in this study, and the results showed that the enrichment level of H3K9me2 at the N-methylated purine-DNA-glycosylase (MPG), X-ray repair cross-complementary gene 1 (XRCC1), and polyadenylate diphosphate ribose polymerase-1 (PARP1) promoter regions of base-excision repair (BER) genes was increased, which inhibited the expression of these BER genes, thereby inhibiting the repair of DNA damage and aggravating the DNA damage. Furthermore, the molecular mechanism by which H3K9me2 participates in the BER repair of arsenic-induced DNA damage was verified based on functional loss and gain experiments. In addition, Ginkgo biloba extract can upregulate the expression of MPG, XRCC1, and PARP1 and ameliorate cell DNA damage by reducing the enrichment of H3K9me2 at repair gene promoter regions.
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Affiliation(s)
- Xuejiao Ding
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, China
- The First Affiliated Hospital of Jiangxi Medical College, Shangrao, Jiangxi, China
| | - Anliu Zhang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, China
- Guiyang Center for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Changzhe Li
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, China
| | - Lu Ma
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, China
| | - Shunfang Tang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, China
| | - Qi Wang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, China
| | - Guanghong Yang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, China
| | - Jun Li
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, 550025, China
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61
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Cai S, Quan S, Yang G, Chen M, Ye Q, Wang G, Yu H, Wang Y, Qiao S, Zeng X. Nutritional Status Impacts Epigenetic Regulation in Early Embryo Development: A Scoping Review. Adv Nutr 2021; 12:1877-1892. [PMID: 33873200 PMCID: PMC8483970 DOI: 10.1093/advances/nmab038] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/03/2021] [Accepted: 03/11/2021] [Indexed: 12/12/2022] Open
Abstract
With the increasing maternal age and the use of assisted reproductive technology in various countries worldwide, the influence of epigenetic modification on embryonic development is increasingly notable and prominent. Epigenetic modification disorders caused by various nutritional imbalance would cause embryonic development abnormalities and even have an indelible impact on health in adulthood. In this scoping review, we summarize the main epigenetic modifications in mammals and the synergies among different epigenetic modifications, especially DNA methylation, histone acetylation, and histone methylation. We performed an in-depth analysis of the regulation of various epigenetic modifications on mammals from zygote formation to cleavage stage and blastocyst stage, and reviewed the modifications of key sites and their potential molecular mechanisms. In addition, we discuss the effects of nutrition (protein, lipids, and one-carbon metabolism) on epigenetic modification in embryos and emphasize the importance of various nutrients in embryonic development and epigenetics during pregnancy. Failures in epigenetic regulation have been implicated in mammalian and human early embryo loss and disease. With the use of reproductive technologies, it is becoming even more important to establish developmentally competent embryos. Therefore, it is essential to evaluate the extent to which embryos are sensitive to these epigenetic modifications and nutrition status. Understanding the epigenetic regulation of early embryo development will help us make better use of reproductive technologies and nutrition regulation to improve reproductive health in mammals.
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Affiliation(s)
- Shuang Cai
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Shuang Quan
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Guangxin Yang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Meixia Chen
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Qianhong Ye
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Gang Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Haitao Yu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Yuming Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, China,Beijing Key Laboratory of Bio-feed Additives, China Agricultural University, Beijing, China
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Stäubli A, Peters AHFM. Mechanisms of maternal intergenerational epigenetic inheritance. Curr Opin Genet Dev 2021; 67:151-162. [DOI: 10.1016/j.gde.2021.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/20/2022]
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63
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Keenen MM, Brown D, Brennan LD, Renger R, Khoo H, Carlson CR, Huang B, Grill SW, Narlikar GJ, Redding S. HP1 proteins compact DNA into mechanically and positionally stable phase separated domains. eLife 2021; 10:e64563. [PMID: 33661100 PMCID: PMC7932698 DOI: 10.7554/elife.64563] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
In mammals, HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1α, HP1β, and HP1γ, display rapid on-off dynamics. Here, we investigate whether phase-separation by HP1 proteins can explain these biological observations. Using bulk and single-molecule methods, we show that, within phase-separated HP1α-DNA condensates, HP1α acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates are resistant to large forces yet can be readily dissolved by HP1β. Finally, we find that differences in each HP1 paralog's DNA compaction and phase-separation properties arise from their respective disordered regions. Our findings suggest a generalizable model for genome organization in which a pool of weakly bound proteins collectively capitalize on the polymer properties of DNA to produce self-organizing domains that are simultaneously resistant to large forces at the mesoscale and susceptible to competition at the molecular scale.
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Affiliation(s)
- Madeline M Keenen
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - David Brown
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Lucy D Brennan
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Roman Renger
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Harrison Khoo
- Department of Mechanical Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Christopher R Carlson
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Physiology, University of California, San FranciscoSan FranciscoUnited States
| | - Bo Huang
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Cluster of Excellence Physics of Life, Technische Universität DresdenDresdenGermany
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Marine Biological LaboratoryWoods HoleUnited States
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Yurdagul A, Kong N, Gerlach BD, Wang X, Ampomah P, Kuriakose G, Tao W, Shi J, Tabas I. ODC (Ornithine Decarboxylase)-Dependent Putrescine Synthesis Maintains MerTK (MER Tyrosine-Protein Kinase) Expression to Drive Resolution. Arterioscler Thromb Vasc Biol 2021; 41:e144-e159. [PMID: 33406854 PMCID: PMC8034502 DOI: 10.1161/atvbaha.120.315622] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE ODC (ornithine decarboxylase)-dependent putrescine synthesis promotes the successive clearance of apoptotic cells (ACs) by macrophages, contributing to inflammation resolution. However, it remains unknown whether ODC is required for other arms of the resolution program. Approach and Results: RNA sequencing of ODC-deficient macrophages exposed to ACs showed increases in mRNAs associated with heightened inflammation and decreases in mRNAs related to resolution and repair compared with WT (wild type) macrophages. In zymosan peritonitis, myeloid ODC deletion led to delayed clearance of neutrophils and a decrease in the proresolving cytokine, IL (interleukin)-10. Nanoparticle-mediated silencing of macrophage ODC in a model of atherosclerosis regression lowered IL-10 expression, decreased efferocytosis, enhanced necrotic core area, and reduced fibrous cap thickness. Mechanistically, ODC deletion lowered basal expression of MerTK (MER tyrosine-protein kinase)-an AC receptor-via a histone methylation-dependent transcriptional mechanism. Owing to lower basal MerTK, subsequent exposure to ACs resulted in lower MerTK-Erk (extracellular signal-regulated kinase) 1/2-dependent IL-10 production. Putrescine treatment of ODC-deficient macrophages restored the expression of both MerTK and AC-induced IL-10. CONCLUSIONS These findings demonstrate that ODC-dependent putrescine synthesis in macrophages maintains a basal level of MerTK expression needed to optimally resolve inflammation upon subsequent AC exposure. Graphic Abstract: A graphic abstract is available for this article.
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Affiliation(s)
- Arif Yurdagul
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Brennan D. Gerlach
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiaobo Wang
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Patrick Ampomah
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - George Kuriakose
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jinjun Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Ira Tabas
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
- Department of Physiology, Columbia University Irving Medical Center, New York, NY 10032, USA
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65
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Tien CL, Mohammadparast S, Chang C. Heterochromatin protein 1 beta regulates neural and neural crest development by repressing pluripotency-associated gene pou5f3.2/oct25 in Xenopus. Dev Dyn 2021; 250:1113-1124. [PMID: 33595886 DOI: 10.1002/dvdy.319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Heterochromatin protein 1 (HP1) is associated with and plays a role in compact chromatin conformation, but the function of HP1 in vertebrate embryogenesis is not understood completely. RESULTS Here, we explore the activity of HP1 in early neural development in the frog Xenopus laevis. We show that the three isoforms of HP1, HP1α, β, and γ, are expressed in similar patterns in the neural and neural crest derivatives in early embryos. Despite this, knockdown of HP1β and HP1γ, but not HP1α, in presumptive neural tissues leads to head defects. Late pan-neural markers and neural crest specifier genes are reduced, but early neural and neural plate border genes are less affected in the morphant embryos. Further investigation reveals that neuronal differentiation is impaired and a pluripotency-associated gene, pou5f3.2/oct25, is expanded in HP1β morphants. Ectopic expression of pou5f3.2/oct25 mimics the effect of HP1β knockdown on marker expression, whereas simultaneous knockdown of HP1β and pou5f3.2/oct25 partially rescues expression of these genes. CONCLUSION Taken together, the data suggest that HP1β regulates transition from precursor to more differentiated cell types during neural and neural crest development in Xenopus, and it does so at least partially via repression of the pluripotency-associated transcription regulator pou5f3.2/oct25.
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Affiliation(s)
- Chih-Liang Tien
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Saeid Mohammadparast
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Chenbei Chang
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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66
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Zhang S, Yu X, Zhang Y, Xue X, Yu Q, Zha Z, Gogol M, Workman JL, Li S. Metabolic regulation of telomere silencing by SESAME complex-catalyzed H3T11 phosphorylation. Nat Commun 2021; 12:594. [PMID: 33500413 PMCID: PMC7838282 DOI: 10.1038/s41467-020-20711-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Telomeres are organized into a heterochromatin structure and maintenance of silent heterochromatin is required for chromosome stability. How telomere heterochromatin is dynamically regulated in response to stimuli remains unknown. Pyruvate kinase Pyk1 forms a complex named SESAME (Serine-responsive SAM-containing Metabolic Enzyme complex) to regulate gene expression by phosphorylating histone H3T11 (H3pT11). Here, we identify a function of SESAME in regulating telomere heterochromatin structure. SESAME phosphorylates H3T11 at telomeres, which maintains SIR (silent information regulator) complex occupancy at telomeres and protects Sir2 from degradation by autophagy. Moreover, SESAME-catalyzed H3pT11 directly represses autophagy-related gene expression to further prevent autophagy-mediated Sir2 degradation. By promoting H3pT11, serine increases Sir2 protein levels and enhances telomere silencing. Loss of H3pT11 leads to reduced Sir2 and compromised telomere silencing during chronological aging. Together, our study provides insights into dynamic regulation of silent heterochromatin by histone modifications and autophagy in response to cell metabolism and aging.
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Affiliation(s)
- Shihao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Yuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xiangyan Xue
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Zitong Zha
- Human Aging Research Institute (HARI), School of Life Science, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Madelaine Gogol
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
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67
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Van MV, Fujimori T, Bintu L. Nanobody-mediated control of gene expression and epigenetic memory. Nat Commun 2021; 12:537. [PMID: 33483487 PMCID: PMC7822885 DOI: 10.1038/s41467-020-20757-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/15/2020] [Indexed: 01/10/2023] Open
Abstract
Targeting chromatin regulators to specific genomic locations for gene control is emerging as a powerful method in basic research and synthetic biology. However, many chromatin regulators are large, making them difficult to deliver and combine in mammalian cells. Here, we develop a strategy for gene control using small nanobodies that bind and recruit endogenous chromatin regulators to a gene. We show that an antiGFP nanobody can be used to simultaneously visualize GFP-tagged chromatin regulators and control gene expression, and that nanobodies against HP1 and DNMT1 can silence a reporter gene. Moreover, combining nanobodies together or with other regulators, such as DNMT3A or KRAB, can enhance silencing speed and epigenetic memory. Finally, we use the slow silencing speed and high memory of antiDNMT1 to build a signal duration timer and recorder. These results set the basis for using nanobodies against chromatin regulators for controlling gene expression and epigenetic memory.
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Affiliation(s)
- Mike V Van
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Taihei Fujimori
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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68
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Zaidan NZ, Sridharan R. HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells. Nucleic Acids Res 2020; 48:12660-12674. [PMID: 33237287 PMCID: PMC7736818 DOI: 10.1093/nar/gkaa1091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/12/2020] [Accepted: 10/27/2020] [Indexed: 01/01/2023] Open
Abstract
The heterochromatin protein 1 (HP1) family members are canonical effectors and propagators of gene repression mediated by histone H3 lysine 9 (H3K9) methylation. HP1γ exhibits an increased interaction with active transcription elongation-associated factors in embryonic stem cells (ESCs) compared to somatic cells. However, whether this association has a functional consequence remains elusive. Here we find that genic HP1γ colocalizes and enhances enrichment of transcription elongation-associated H3K36me3 rather than H3K9me3. Unexpectedly, sustained H3K36me3 deposition is dependent on HP1γ. HP1γ-deleted ESCs display reduced H3K36me3 enrichment, concomitant with decreased expression at shared genes which function to maintain cellular homeostasis. Both the H3K9me3-binding chromodomain and histone binding ability of HP1γ are dispensable for maintaining H3K36me3 levels. Instead, the chromoshadow together with the hinge domain of HP1γ that confer protein and nucleic acid-binding ability are sufficient because they retain the ability to interact with NSD1, an H3K36 methyltransferase. HP1γ-deleted ESCs have a slower self-renewal rate and an impaired ability to differentiate towards cardiac mesoderm. Our findings reveal a requirement for HP1γ in faithful establishment of transcription elongation in ESCs, which regulates pluripotency.
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Affiliation(s)
- Nur Zafirah Zaidan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.,Genetics Training Program, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53715, USA
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69
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Kurup JT, Han Z, Jin W, Kidder BL. H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells. Development 2020; 147:dev.188516. [PMID: 33144397 DOI: 10.1242/dev.188516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022]
Abstract
Heterochromatin, a densely packed chromatin state that is transcriptionally silent, is a critical regulator of gene expression. However, it is unclear how the repressive histone modification H4K20me3 or the histone methyltransferase SUV420H2 regulates embryonic stem (ES) cell fate by patterning the epigenetic landscape. Here, we report that depletion of SUV420H2 leads to a near-complete loss of H4K20me3 genome wide, dysregulated gene expression and delayed ES cell differentiation. SUV420H2-bound regions are enriched with repetitive DNA elements, which are de-repressed in SUV420H2 knockout ES cells. Moreover, SUV420H2 regulation of H4K20me3-marked heterochromatin controls chromatin architecture, including fine-scale chromatin interactions in pluripotent ES cells. Our results indicate that SUV420H2 plays a crucial role in stabilizing the three-dimensional chromatin landscape of ES cells, as loss of SUV420H2 resulted in A/B compartment switching, perturbed chromatin insulation, and altered chromatin interactions of pericentric heterochromatin and surrounding regions, indicative of localized decondensation. In addition, depletion of SUV420H2 resulted in compromised interactions between H4K20me3 and gene-regulatory regions. Together, these findings describe a new role for SUV420H2 in regulating the chromatin landscape of ES cells.
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Affiliation(s)
- Jiji T Kurup
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Zhijun Han
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenfei Jin
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA .,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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70
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Ding Q, Koren A. Positive and Negative Regulation of DNA Replication Initiation. Trends Genet 2020; 36:868-879. [PMID: 32739030 PMCID: PMC7572746 DOI: 10.1016/j.tig.2020.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
Genomic DNA is replicated every cell cycle by the programmed activation of replication origins at specific times and chromosomal locations. The factors that define the locations of replication origins and their typical activation times in eukaryotic cells are poorly understood. Previous studies highlighted the role of activating factors and epigenetic modifications in regulating replication initiation. Here, we review the role that repressive pathways - and their alleviation - play in establishing the genomic landscape of replication initiation. Several factors mediate this repression, in particular, factors associated with inactive chromatin. Repression can support organized, yet stochastic, replication initiation, and its absence could explain instances of rapid and random replication or re-replication.
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Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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71
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Ma S, Zhang Y. Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq. MOLECULAR BIOMEDICINE 2020; 1:9. [PMID: 34765994 PMCID: PMC7546943 DOI: 10.1186/s43556-020-00009-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022] Open
Abstract
Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) have enabled us to dissect the pan-genomic regulatory landscape of cells and tissues in both time and space dimensions by detecting specific chromatin state and its corresponding transcription factors. Pioneered by the advancement of chromatin immunoprecipitation-chip (ChIP-chip) technology, abundant epigenome profiling technologies have become available such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single-cell sequencing has revolutionized the next-generation sequencing, applications in single-cell epigenetics are enriched rapidly. Epigenome sequencing technologies have evolved from low-throughput to high-throughput and from bulk sample to the single-cell scope, which unprecedentedly benefits scientists to interpret life from different angles. In this review, after briefly introducing the background knowledge of epigenome biology, we discuss the development of epigenome sequencing technologies, especially ChIP-seq & ATAC-seq and their current applications in scientific research. Finally, we provide insights into future applications and challenges.
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Affiliation(s)
- Shaoqian Ma
- School of Life Sciences, Xiamen University, Xiamen, 361102 Fujian China
| | - Yongyou Zhang
- School of Life Sciences, Xiamen University, Xiamen, 361102 Fujian China
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72
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Singh PB, Belyakin SN, Laktionov PP. Biology and Physics of Heterochromatin- Like Domains/Complexes. Cells 2020; 9:E1881. [PMID: 32796726 PMCID: PMC7465696 DOI: 10.3390/cells9081881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 11/17/2022] Open
Abstract
The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin template-dependent processes. Domains are more than 100 kb in size; complexes less than 100 kb. They are present in the genomes of organisms ranging from fission yeast to human, with an expansion in size and number in mammals. Some of the likely functions of domains/complexes include silencing of the donor mating type region in fission yeast, preservation of DNA methylation at imprinted germline differentially methylated regions (gDMRs) and regulation of the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. A thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes may require a gestalt shift away from the monomer as the "unit of incompatibility" that determines the sign and magnitude of the Flory-Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal "clutch", consisting of between 2 and 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of "clutches" in a domain/complex. Our approach could provide an additional tool for understanding the biophysics of the 3D genome.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, Nur-Sultan City 010000, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Stepan N. Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
| | - Petr P. Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
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73
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Meyer-Nava S, Nieto-Caballero VE, Zurita M, Valadez-Graham V. Insights into HP1a-Chromatin Interactions. Cells 2020; 9:E1866. [PMID: 32784937 PMCID: PMC7465937 DOI: 10.3390/cells9081866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022] Open
Abstract
Understanding the packaging of DNA into chromatin has become a crucial aspect in the study of gene regulatory mechanisms. Heterochromatin establishment and maintenance dynamics have emerged as some of the main features involved in genome stability, cellular development, and diseases. The most extensively studied heterochromatin protein is HP1a. This protein has two main domains, namely the chromoshadow and the chromodomain, separated by a hinge region. Over the years, several works have taken on the task of identifying HP1a partners using different strategies. In this review, we focus on describing these interactions and the possible complexes and subcomplexes associated with this critical protein. Characterization of these complexes will help us to clearly understand the implications of the interactions of HP1a in heterochromatin maintenance, heterochromatin dynamics, and heterochromatin's direct relationship to gene regulation and chromatin organization.
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Affiliation(s)
| | | | | | - Viviana Valadez-Graham
- Instituto de Biotecnología, Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62210, Mexico; (S.M.-N.); (V.E.N.-C.); (M.Z.)
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74
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Abstract
As a unique subpopulation of cancer cells, cancer stem cells (CSCs) acquire the resistance to conventional therapies and appear to be the prime cause of cancer recurrence. Like their normal counterparts, CSCs can renew themselves and generate differentiated progenies. Cancer stem cells are distinguished among heterogenous cancer cells by molecular markers and their capacity of efficiently forming new tumors composed of diverse and heterogenous cancer cells. Tumor heterogeneity can be inter- or intra-tumor, molecularly resulting from the accumulation of genetic and non-genetic alterations. Non-genetic alterations are mainly changes on epigenetic modifications of DNA and histone, and chromatin remodeling. As tumor-initiating cells and contributing to the tumor heterogeneity in the brain, glioblastoma stem cells (GSCs) attract extensive research interests. Epigenetic modifications confer on tumor cells including CSCs reversible and inheritable genomic changes and affect gene expression without alteration in DNA sequence. Here, we will review recent advances in histone demethylation, DNA methylation, RNA methylation and ubiquitination in glioblastomas and their impacts on tumorigenesis with a focus on CSCs.
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Affiliation(s)
- Kezhou Zhu
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Victoria Xie
- M.D. Program, Baylor College of Medicine, Houston, TX, United States
| | - Suyun Huang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
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75
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Yen WF, Sharma R, Cols M, Lau CM, Chaudhry A, Chowdhury P, Yewdell WT, Vaidyanathan B, Sun A, Coffre M, Pucella JN, Chen CC, Jasin M, Sun JC, Rudensky AY, Koralov SB, Chaudhuri J. Distinct Requirements of CHD4 during B Cell Development and Antibody Response. Cell Rep 2020; 27:1472-1486.e5. [PMID: 31042474 PMCID: PMC6527137 DOI: 10.1016/j.celrep.2019.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/15/2019] [Accepted: 04/01/2019] [Indexed: 11/21/2022] Open
Abstract
The immunoglobulin heavy chain (Igh) locus features a dynamic chromatin landscape to promote class switch recombination (CSR), yet the mechanisms that regulate this landscape remain poorly understood. CHD4, a component of the chromatin remodeling NuRD complex, directly binds H3K9me3, an epigenetic mark present at the Igh locus during CSR. We find that CHD4 is essential for early B cell development but is dispensable for the homeostatic maintenance of mature, naive B cells. However, loss of CHD4 in mature B cells impairs CSR because of suboptimal targeting of AID to the Igh locus. Additionally, we find that CHD4 represses p53 expression to promote B cell proliferation. This work reveals distinct roles for CHD4 in B cell development and CSR and links the H3K9me3 epigenetic mark with AID recruitment to the Igh locus. Yen et al. demonstrate that CHD4, a component of the NuRD remodeling complex, is essential for early B cell development, represses p53 expression in mature B cells, and influences the recruitment of AID to DNA during class switch recombination.
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Affiliation(s)
- Wei-Feng Yen
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Biochemistry, Cellular and Molecular Biology Program, Weill Graduate School of Medical Sciences, New York, NY, USA
| | - Rahul Sharma
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Montserrat Cols
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Colleen M Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashutosh Chaudhry
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Priyanka Chowdhury
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - William T Yewdell
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bharat Vaidyanathan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Amy Sun
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Maryaline Coffre
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Joseph N Pucella
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA
| | - Chun-Chin Chen
- Biochemistry, Cellular and Molecular Biology Program, Weill Graduate School of Medical Sciences, New York, NY, USA; Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Jasin
- Biochemistry, Cellular and Molecular Biology Program, Weill Graduate School of Medical Sciences, New York, NY, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA; Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA
| | - Alexander Y Rudensky
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA; Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA.
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76
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Lerner J, Gomez-Garcia PA, McCarthy RL, Liu Z, Lakadamyali M, Zaret KS. Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin. Mol Cell 2020; 79:677-688.e6. [PMID: 32574554 DOI: 10.1016/j.molcel.2020.05.036] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 04/06/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Abstract
Enzymatic probes of chromatin structure reveal accessible versus inaccessible chromatin states, while super-resolution microscopy reveals a continuum of chromatin compaction states. Characterizing histone H2B movements by single-molecule tracking (SMT), we resolved chromatin domains ranging from low to high mobility and displaying different subnuclear localizations patterns. Heterochromatin constituents correlated with the lowest mobility chromatin, whereas transcription factors varied widely with regard to their respective mobility with low- or high-mobility chromatin. Pioneer transcription factors, which bind nucleosomes, can access the low-mobility chromatin domains, whereas weak or non-nucleosome binding factors are excluded from the domains and enriched in higher mobility domains. Nonspecific DNA and nucleosome binding accounted for most of the low mobility of strong nucleosome interactor FOXA1. Our analysis shows how the parameters of the mobility of chromatin-bound factors, but not their diffusion behaviors or SMT-residence times within chromatin, distinguish functional characteristics of different chromatin-interacting proteins.
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Affiliation(s)
- Jonathan Lerner
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Pablo Aurelio Gomez-Garcia
- Center for Genomic Regulation, Barcelona Biomedical Research Park, 08003 Barcelona, Spain; ICFO-Institute of Photonics Sciences, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ryan L McCarthy
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Zhe Liu
- HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Melike Lakadamyali
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA; University of Pennsylvania, Department of Physiology, Philadelphia, PA 19104-6058, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA.
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77
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Bioinformatics analysis of the network of histone H3 lysine 9 trimethylation in acute myeloid leukaemia. Oncol Rep 2020; 44:543-554. [PMID: 32468066 PMCID: PMC7336454 DOI: 10.3892/or.2020.7627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
Changes in histone H3 lysine 9 trimethylation (H3K9me3) may be related to the development of drug-resistant acute myeloid leukaemia (AML); insights into the network of H3K9me3 may improve patient prognosis. Patient data were derived from the Gene Expression Omnibus (GEO) database and data from AML cells treated with chidamide, a novel benzamide chemical class of histone deacetylase inhibitor (HDACi), in vitro were derived from ChIP-seq. Patients and AML cell data were analysed using GEO2R, GOseq, KOBAS, the STRING database and Cytoscape 3.5.1. We identified several genes related to the upregulation or downregulation of H3K9me3 in AML patients; some of these genes were related to apoptosis, autophagy, and the pathway of cell longevity. AML cells treated with chidamide in vitro showed the same gene changes. The protein interactions in the network did not have significantly more interactions than expected, suggesting the need for more research to identify these interactions. One compelling result from the protein interaction study was that sirtuin 1 (SIRT1) may have an indirect interaction with lysine-specific demethylase 4A (KDM4A). These results help explain alterations of H3K9me3 in AML that may direct further studies aimed at improving patient prognosis. These results may also provide a basis for chidamide as a treatment strategy for AML patients in the future.
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78
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Shukla A, Ramirez NGP, D’Orso I. HIV-1 Proviral Transcription and Latency in the New Era. Viruses 2020; 12:v12050555. [PMID: 32443452 PMCID: PMC7291205 DOI: 10.3390/v12050555] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
Three decades of extensive work in the HIV field have revealed key viral and host cell factors controlling proviral transcription. Various models of transcriptional regulation have emerged based on the collective information from in vitro assays and work in both immortalized and primary cell-based models. Here, we provide a recount of the past and current literature, highlight key regulatory aspects, and further describe potential limitations of previous studies. We particularly delve into critical steps of HIV gene expression including the role of the integration site, nucleosome positioning and epigenomics, and the transition from initiation to pausing and pause release. We also discuss open questions in the field concerning the generality of previous regulatory models to the control of HIV transcription in patients under suppressive therapy, including the role of the heterogeneous integration landscape, clonal expansion, and bottlenecks to eradicate viral persistence. Finally, we propose that building upon previous discoveries and improved or yet-to-be discovered technologies will unravel molecular mechanisms of latency establishment and reactivation in a “new era”.
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79
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Pessoa Rodrigues C, Herman JS, Herquel B, Valsecchi CIK, Stehle T, Grün D, Akhtar A. Temporal expression of MOF acetyltransferase primes transcription factor networks for erythroid fate. SCIENCE ADVANCES 2020; 6:eaaz4815. [PMID: 32671208 PMCID: PMC7314555 DOI: 10.1126/sciadv.aaz4815] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/09/2020] [Indexed: 05/03/2023]
Abstract
Self-renewal and differentiation of hematopoietic stem cells (HSCs) are orchestrated by the combinatorial action of transcription factors and epigenetic regulators. Here, we have explored the mechanism by which histone H4 lysine 16 acetyltransferase MOF regulates erythropoiesis. Single-cell RNA sequencing and chromatin immunoprecipitation sequencing uncovered that MOF influences erythroid trajectory by dynamic recruitment to chromatin and its haploinsufficiency causes accumulation of a transient HSC population. A regulatory network consisting of MOF, RUNX1, and GFI1B is critical for erythroid fate commitment. GFI1B acts as a Mof activator which is necessary and sufficient for cell type-specific induction of Mof expression. Plasticity of Mof-depleted HSCs can be rescued by expression of a downstream effector, Gata1, or by rebalancing acetylation via a histone deacetylase inhibitor. Accurate timing and dosage of Mof expression act as a rheostat for the feedforward transcription factor network that safeguards progression along the erythroid fate.
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Affiliation(s)
- Cecilia Pessoa Rodrigues
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- University of Freiburg, Faculty of Biology, Schaenzlestrasse 1, 79104 Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
| | - Josip Stefan Herman
- University of Freiburg, Faculty of Biology, Schaenzlestrasse 1, 79104 Freiburg, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB), Freiburg, Germany
- Laboratory of Quantitative Single-Cell Biology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Benjamin Herquel
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Thomas Stehle
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Dominic Grün
- Laboratory of Quantitative Single-Cell Biology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- CIBSS—Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
- CIBSS—Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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80
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Adoue V, Joffre O. [Endogenous retroviruses: friend or foe of the immune system?]. Med Sci (Paris) 2020; 36:253-260. [PMID: 32228844 DOI: 10.1051/medsci/2020022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Upon priming by dendritic cells, naïve CD4 T lymphocytes are exposed to distinct molecular environments depending on the nature of the pathological stimulus. In response, they mobilize different gene networks that establish lineage-specific developmental programs, and coordinate the acquisition of specific phenotype and functions. Accordingly, CD4 T cells are capable of differentiation into a large variety of functionally-distinct T helper (Th) cell subsets. In this review, we describe the molecular events that control CD4 T cell differentiation at the level of the chromatin. We insist on recent works that have highlighted the key role of H3K9me3-dependent epigenetic mechanisms in the regulation of T cell identity. Interestingly, these pathways shape and control the developmental programs at least in part through the regulation of endogenous retroviruses-derived sequences that have been exapted into cis-regulatory modules of Th genes.
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Affiliation(s)
- Véronique Adoue
- Centre de Physiopathologie Toulouse Purpan, Inserm U1043 - BP 3028, 31024 Toulouse Cedex 3, France
| | - Olivier Joffre
- Centre de Physiopathologie Toulouse Purpan, Inserm U1043 - BP 3028, 31024 Toulouse Cedex 3, France
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81
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Kumar A, Kono H. Heterochromatin protein 1 (HP1): interactions with itself and chromatin components. Biophys Rev 2020; 12:387-400. [PMID: 32144738 PMCID: PMC7242596 DOI: 10.1007/s12551-020-00663-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/23/2020] [Indexed: 12/12/2022] Open
Abstract
Isoforms of heterochromatin protein 1 (HP1) have been known to perform a multitude of functions ranging from gene silencing, gene activation to cell cycle regulation, and cell differentiation. This functional diversity arises from the dissimilarities coded in protein sequence which confers different biophysical and biochemical properties to individual structural elements of HP1 and thereby different behavior and interaction patterns. Hence, an understanding of various interactions of the structural elements of HP1 will be of utmost importance to better elucidate chromatin dynamics in its presence. In this review, we have gathered available information about interactions of HP1 both within and with itself as well as with chromatin elements. Also, the possible implications of these interactions are discussed.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Group, Institute for Quantum Life Science (iQLS), National Institutes for Quantum and Radiological Science and Technology (QST), Kizugawa, Kyoto, 619-0215, Japan.
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82
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Galigniana NM, Charó NL, Uranga R, Cabanillas AM, Piwien-Pilipuk G. Oxidative stress induces transcription of telomeric repeat-containing RNA (TERRA) by engaging PKA signaling and cytoskeleton dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118643. [DOI: 10.1016/j.bbamcr.2020.118643] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022]
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83
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Yi D, Nguyen HP, Sul HS. Epigenetic dynamics of the thermogenic gene program of adipocytes. Biochem J 2020; 477:1137-1148. [PMID: 32219439 PMCID: PMC8594062 DOI: 10.1042/bcj20190599] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
Brown adipose tissue (BAT) is a metabolically beneficial organ capable of burning fat by dissipating chemical energy into heat, thereby increasing energy expenditure. Moreover, subcutaneous white adipose tissue can undergo so-called browning/beiging. The recent recognition of the presence of brown or beige adipocytes in human adults has attracted much attention to elucidate the molecular mechanism underlying the thermogenic adipose program. Many key transcriptional regulators critical for the thermogenic gene program centering on activating the UCP1 promoter, have been discovered. Thermogenic gene expression in brown adipocytes rely on co-ordinated actions of a multitude of transcription factors, including EBF2, PPARγ, Zfp516 and Zc3h10. These transcription factors probably integrate into a cohesive network for BAT gene program. Moreover, these transcription factors recruit epigenetic factors, such as LSD1 and MLL3/4, for specific histone signatures to establish the favorable chromatin landscape. In this review, we discuss advances made in understanding the molecular mechanism underlying the thermogenic gene program, particularly epigenetic regulation.
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Affiliation(s)
- Danielle Yi
- Department of Nutritional Sciences and Toxicology and Endocrinology Program, University of California, Berkeley, CA 94720, U.S.A
| | - Hai P Nguyen
- Department of Nutritional Sciences and Toxicology and Endocrinology Program, University of California, Berkeley, CA 94720, U.S.A
| | - Hei Sook Sul
- Department of Nutritional Sciences and Toxicology and Endocrinology Program, University of California, Berkeley, CA 94720, U.S.A
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84
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Small RNAs in the Transgenerational Inheritance of Epigenetic Information. Trends Genet 2020; 36:203-214. [DOI: 10.1016/j.tig.2019.12.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/19/2019] [Accepted: 12/06/2019] [Indexed: 01/21/2023]
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85
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The mouse HP1 proteins are essential for preventing liver tumorigenesis. Oncogene 2020; 39:2676-2691. [PMID: 32020053 DOI: 10.1038/s41388-020-1177-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 01/06/2020] [Accepted: 01/21/2020] [Indexed: 12/16/2022]
Abstract
Chromatin organization is essential for appropriate interpretation of the genetic information. Here, we demonstrated that the chromatin-associated proteins HP1 are dispensable for hepatocytes survival but are essential within hepatocytes to prevent liver tumor development in mice with HP1β being pivotal in these functions. Yet, we found that the loss of HP1 per se is not sufficient to induce cell transformation but renders cells more resistant to specific stress such as the expression of oncogenes and thus in fine, more prone to cell transformation. Molecular characterization of HP1-Triple KO premalignant livers and BMEL cells revealed that HP1 are essential for the maintenance of heterochromatin organization and for the regulation of specific genes with most of them having well characterized functions in liver functions and homeostasis. We further showed that some specific retrotransposons get reactivated upon loss of HP1, correlating with overexpression of genes in their neighborhood. Interestingly, we found that, although HP1-dependent genes are characterized by enrichment H3K9me3, this mark does not require HP1 for its maintenance and is not sufficient to maintain gene repression in absence of HP1. Finally, we demonstrated that the loss of TRIM28 association with HP1 recapitulated several phenotypes induced by the loss of HP1 including the reactivation of some retrotransposons and the increased incidence of liver cancer development. Altogether, our findings indicate that HP1 proteins act as guardians of liver homeostasis to prevent tumor development by modulating multiple chromatin-associated events within both the heterochromatic and euchromatic compartments, partly through regulation of the corepressor TRIM28 activity.
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86
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Udroiu I, Sgura A. Alternative Lengthening of Telomeres and Chromatin Status. Genes (Basel) 2019; 11:genes11010045. [PMID: 31905921 PMCID: PMC7016797 DOI: 10.3390/genes11010045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/22/2019] [Accepted: 12/23/2019] [Indexed: 12/16/2022] Open
Abstract
Telomere length is maintained by either telomerase, a reverse transcriptase, or alternative lengthening of telomeres (ALT), a mechanism that utilizes homologous recombination (HR) proteins. Since access to DNA for HR enzymes is regulated by the chromatin status, it is expected that telomere elongation is linked to epigenetic modifications. The aim of this review is to elucidate the epigenetic features of ALT-positive cells. In order to do this, it is first necessary to understand the telomeric chromatin peculiarities. So far, the epigenetic nature of telomeres is still controversial: some authors describe them as heterochromatic, while for others, they are euchromatic. Similarly, ALT activity should be characterized by the loss (according to most researchers) or formation (as claimed by a minority) of heterochromatin in telomeres. Besides reviewing the main works in this field and the most recent findings, some hypotheses involving the role of telomere non-canonical sequences and the possible spatial heterogeneity of telomeres are given.
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87
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Grigoryev SA, Popova EY. Attraction of Likenesses: Mechanisms of Self-Association and Compartmentalization of Eukaryotic Chromatin. Mol Biol 2019. [DOI: 10.1134/s0026893319060050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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88
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Maksimov DA, Koryakov DE. Binding of SU(VAR)3-9 Partially Depends on SETDB1 in the Chromosomes of Drosophila melanogaster. Cells 2019; 8:cells8091030. [PMID: 31491894 PMCID: PMC6769583 DOI: 10.3390/cells8091030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023] Open
Abstract
H3K9 methylation is known to play a critical role in gene silencing. This modification is established and maintained by several enzymes, but relationships between them are not fully understood. In the present study, we decipher the interplay between two Drosophila H3K9-specific histone methyltransferases, SU(VAR)3-9 and SETDB1. We asked whether SETDB1 is required for targeting of SU(VAR)3-9. Using DamID-seq, we obtained SU(VAR)3-9 binding profiles for the chromosomes from larval salivary glands and germline cells from adult females, and compared profiles between the wild type and SETDB1-mutant backgrounds. Our analyses indicate that the vast majority of single copy genes in euchromatin are targeted by SU(VAR)3-9 only in the presence of SETDB1, whereas SU(VAR)3-9 binding at repeated sequences in heterochromatin is largely SETDB1-independent. Interestingly, piRNA clusters 42AB and 38C in salivary gland chromosomes bind SU(VAR)3-9 regardless of SETDB1, whereas binding to the same regions in the germline cells is SETDB1-dependent. In addition, we compared SU(VAR)3-9 profiles in female germline cells at different developmental stages (germarium cells in juvenile ovaries and mature nurse cells). It turned out that SU(VAR)3-9 binding is influenced both by the presence of SETDB1, as well as by the differentiation stage.
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Affiliation(s)
- Daniil A Maksimov
- Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia.
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Dmitry E Koryakov
- Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia.
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89
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Monaghan L, Massett ME, Bunschoten RP, Hoose A, Pirvan PA, Liskamp RMJ, Jørgensen HG, Huang X. The Emerging Role of H3K9me3 as a Potential Therapeutic Target in Acute Myeloid Leukemia. Front Oncol 2019; 9:705. [PMID: 31428579 PMCID: PMC6687838 DOI: 10.3389/fonc.2019.00705] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/16/2019] [Indexed: 12/23/2022] Open
Abstract
Growing evidence has demonstrated that epigenetic dysregulation is a common pathological feature in human cancer cells. Global alterations in the epigenetic landscape are prevalent in malignant cells across different solid tumors including, prostate cancer, non-small-cell lung cancer, renal cell carcinoma, and in haemopoietic malignancy. In particular, DNA hypomethylation and histone hypoacetylation have been observed in acute myeloid leukemia (AML) patient blasts, with histone methylation being an emerging area of study. Histone 3 lysine 9 trimethylation (H3K9me3) is a post-translational modification known to be involved in the regulation of a broad range of biological processes, including the formation of transcriptionally silent heterochromatin. Following the observation of its aberrant methylation status in hematological malignancy and several other cancer phenotypes, recent studies have associated H3K9me3 levels with patient outcome and highlighted key molecular mechanisms linking H3K9me3 profile with AML etiology in a number of large-scale meta-analysis. Consequently, the development and application of small molecule inhibitors which target the histone methyltransferases or demethylase enzymes known to participate in the oncogenic regulation of H3K9me3 in AML represents an advancing area of ongoing study. Here, we provide a comprehensive review on how this particular epigenetic mark is regulated within cells and its emerging role as a potential therapeutic target in AML, along with an update on the current research into advancing the generation of more potent and selective inhibitors against known H3K9 methyltransferases and demethylases.
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Affiliation(s)
- Laura Monaghan
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Matthew E. Massett
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Alex Hoose
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Heather G. Jørgensen
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Xu Huang
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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90
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Sinton MC, Hay DC, Drake AJ. Metabolic control of gene transcription in non-alcoholic fatty liver disease: the role of the epigenome. Clin Epigenetics 2019; 11:104. [PMID: 31319896 PMCID: PMC6637519 DOI: 10.1186/s13148-019-0702-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/09/2019] [Indexed: 01/30/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is estimated to affect 24% of the global adult population. NAFLD is a major risk factor for the development of cirrhosis and hepatocellular carcinoma, as well as being strongly associated with type 2 diabetes and cardiovascular disease. It has been proposed that up to 88% of obese adults have NAFLD, and with global obesity rates increasing, this disease is set to become even more prevalent. Despite intense research in this field, the molecular processes underlying the pathology of NAFLD remain poorly understood. Hepatic intracellular lipid accumulation may lead to dysregulated tricarboxylic acid (TCA) cycle activity and associated alterations in metabolite levels. The TCA cycle metabolites alpha-ketoglutarate, succinate and fumarate are allosteric regulators of the alpha-ketoglutarate-dependent dioxygenase family of enzymes. The enzymes within this family have multiple targets, including DNA and chromatin, and thus may be capable of modulating gene transcription in response to intracellular lipid accumulation through alteration of the epigenome. In this review, we discuss what is currently understood in the field and suggest areas for future research which may lead to the development of novel preventative or therapeutic interventions for NAFLD.
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Affiliation(s)
- Matthew C Sinton
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - David C Hay
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Amanda J Drake
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
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91
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Jang S, Song JJ. The big picture of chromatin biology by cryo-EM. Curr Opin Struct Biol 2019; 58:76-87. [PMID: 31233978 DOI: 10.1016/j.sbi.2019.05.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/10/2019] [Accepted: 05/20/2019] [Indexed: 01/07/2023]
Abstract
Modifications of chromatin structure are one of the key mechanisms regulating epigenetic gene expression. Proteins involved in chromatin modification mainly function as large multi-subunit complexes, and each component in the complex contributes to the function and activity of the complex. However, little is known about the structures of whole complexes and the mechanisms by which the chromatin-modifying complexes function, the functional roles of each component in the complexes, and how the complexes recognize the central unit of chromatin, the nucleosome. This lack of information is partially due to the lack of structural information for whole complexes. Recent advances in cryo-EM have begun to reveal the structures of whole chromatin-modifying complexes that enable us to understand the big picture of chromatin biology. In this review, we discuss the recent discoveries related to the mechanisms of chromatin-modifying complexes.
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Affiliation(s)
- Seongmin Jang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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92
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MacDonald IA, Butler KV, Herring LE, Clinkscales SE, Yelagandula R, Stecher K, Bell O, Graves LM, Jin J, Hathaway NA. Pathway-Based High-Throughput Chemical Screen Identifies Compounds That Decouple Heterochromatin Transformations. SLAS DISCOVERY 2019; 24:802-816. [PMID: 31145866 DOI: 10.1177/2472555219849838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Heterochromatin protein 1 (HP1) facilitates the formation of repressive heterochromatin domains by recruiting histone lysine methyltransferase enzymes to chromatin, resulting in increased levels of histone H3K9me3. To identify chemical inhibitors of the HP1-heterochromatin gene repression pathway, we combined a cell-based assay that utilized chemical-mediated recruitment of HP1 to an endogenous active gene with high-throughput flow cytometry. Here we characterized small molecule inhibitors that block HP1-mediated heterochromatin formation. Our lead compounds demonstrated dose-dependent inhibition of HP1-stimulated gene repression and were validated in an orthogonal cell-based system. One lead inhibitor was improved by a change in stereochemistry, resulting in compound 2, which was further used to decouple the inverse relationship between H3K9 and H3K4 methylation states. We identified molecular components that bound compound 2, either directly or indirectly, by chemical affinity purification with a biotin-tagged derivative, followed by quantitative proteomic techniques. In summary, our pathway-based chemical screening approach resulted in the discovery of new inhibitors of HP1-mediated heterochromatin formation while identifying exciting new molecular interactions in the pathway to explore in the future. This modular platform can be expanded to test a wide range of chromatin modification pathways yielding inhibitors that are cell permeable and function in a physiologically relevant setting.
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Affiliation(s)
- Ian A MacDonald
- 1 The Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kyle V Butler
- 2 Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura E Herring
- 3 Department of Pharmacology, UNC Michael Hooker Proteomics Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Sarah E Clinkscales
- 1 The Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ramesh Yelagandula
- 4 Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Karin Stecher
- 4 Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Oliver Bell
- 4 Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria.,5 Department of Biochemistry and Molecular Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Lee M Graves
- 3 Department of Pharmacology, UNC Michael Hooker Proteomics Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Jian Jin
- 2 Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathaniel A Hathaway
- 1 The Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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93
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Ben Zouari Y, Molitor AM, Sikorska N, Pancaldi V, Sexton T. ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C. Genome Biol 2019; 20:102. [PMID: 31118054 PMCID: PMC6532271 DOI: 10.1186/s13059-019-1706-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 05/03/2019] [Indexed: 12/19/2022] Open
Abstract
Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks.
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Affiliation(s)
- Yousra Ben Zouari
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
- University of Strasbourg, Illkirch, France
| | - Anne M Molitor
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
- University of Strasbourg, Illkirch, France
| | - Natalia Sikorska
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
- University of Strasbourg, Illkirch, France
| | - Vera Pancaldi
- Centre de Recherches en Cancérologie de Toulouse (CRCT), INSERM U1037, Toulouse, France
- University Paul Sabatier III, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France.
- CNRS UMR7104, Illkirch, France.
- INSERM U1258, Illkirch, France.
- University of Strasbourg, Illkirch, France.
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94
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Zhu Q, Ramakrishnan M, Park J, Belden WJ. Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci. BMC Genomics 2019; 20:350. [PMID: 31068130 PMCID: PMC6505117 DOI: 10.1186/s12864-019-5729-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/24/2019] [Indexed: 01/01/2023] Open
Abstract
Background Histone H3 lysine 4 tri-methylation (H3K4me3) and histone H3 lysine 9 tri-methylation (H3K9me3) are widely perceived to be opposing and often mutually exclusive chromatin modifications. However, both are needed for certain light-activated genes in Neurospora crassa (Neurospora), including frequency (frq) and vivid (vvd). Except for these 2 loci, little is known about how H3K4me3 and H3K9me3 impact and contribute to light-regulated gene expression. Results In this report, we performed a multi-dimensional genomic analysis to understand the role of H3K4me3 and H3K9me3 using the Neurospora light response as the system. RNA-seq on strains lacking H3 lysine 4 methyltransferase (KMT2/SET-1) and histone H3 lysine 9 methyltransferase (KMT1/DIM-5) revealed some light-activated genes had altered expression, but the light response was largely intact. Comparing these 2 mutants to wild-type (WT), we found that roughly equal numbers of genes showed elevated and reduced expression in the dark and the light making the environmental stimulus somewhat ancillary to the genome-wide effects. ChIP-seq experiments revealed H3K4me3 and H3K9me3 had only minor changes in response to light in WT, but there were notable alterations in H3K4me3 in Δkmt1/Δdim-5 and H3K9me3 in Δkmt2/Δset-1 indicating crosstalk and redistribution between the modifications. Integrated analysis of the RNA-seq and ChIP-seq highlighted context-dependent roles for KMT2/SET1 and KMT1/DIM-5 as either co-activators or co-repressors with some overlap as co-regulators. At a small subset of loci, H3K4 methylation is required for H3K9me3-mediated facultative heterochromatin including, the central clock gene frequency (frq). Finally, we used sequential ChIP (re-ChIP) experiment to confirm Neurospora contains K4/K9 bivalent domains. Conclusions Collectively, these data indicate there are obfuscated regulatory roles for H3K4 methylation and H3K9 methylation depending on genome location with some minor overlap and co-dependency. Electronic supplementary material The online version of this article (10.1186/s12864-019-5729-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiaoqiao Zhu
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Mukund Ramakrishnan
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.,Current Address: Department of Biological Sciences, IISER Berhampur, Berhampur, Ganjam, Odisha, 760010, India
| | - Jinhee Park
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - William J Belden
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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95
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Wiese M, Bannister AJ, Basu S, Boucher W, Wohlfahrt K, Christophorou MA, Nielsen ML, Klenerman D, Laue ED, Kouzarides T. Citrullination of HP1γ chromodomain affects association with chromatin. Epigenetics Chromatin 2019; 12:21. [PMID: 30940194 PMCID: PMC6444592 DOI: 10.1186/s13072-019-0265-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/19/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Stem cell differentiation involves major chromatin reorganisation, heterochromatin formation and genomic relocalisation of structural proteins, including heterochromatin protein 1 gamma (HP1γ). As the principal reader of the repressive histone marks H3K9me2/3, HP1 plays a key role in numerous processes including heterochromatin formation and maintenance. RESULTS We find that HP1γ is citrullinated in mouse embryonic stem cells (mESCs) and this diminishes when cells differentiate, indicating that it is a dynamically regulated post-translational modification during stem cell differentiation. Peptidylarginine deiminase 4, a known regulator of pluripotency, citrullinates HP1γ in vitro. This requires R38 and R39 within the HP1γ chromodomain, and the catalytic activity is enhanced by trimethylated H3K9 (H3K9me3) peptides. Mutation of R38 and R39, designed to mimic citrullination, affects HP1γ binding to H3K9me3-containing peptides. Using live-cell single-particle tracking, we demonstrate that R38 and R39 are important for HP1γ binding to chromatin in vivo. Furthermore, their mutation reduces the residence time of HP1γ on chromatin in differentiating mESCs. CONCLUSION Citrullination is a novel post-translational modification of the structural heterochromatin protein HP1γ in mESCs that is dynamically regulated during mESC differentiation. The citrullinated residues lie within the HP1γ chromodomain and are important for H3K9me3 binding in vitro and chromatin association in vivo.
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Affiliation(s)
- Meike Wiese
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
- Max Planck Institute for Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Andrew J. Bannister
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| | - Srinjan Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, CB2 1QR UK
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Kai Wohlfahrt
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Maria A. Christophorou
- Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU UK
| | - Michael L. Nielsen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
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96
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Heterochromatin protein 1 (HP1) is intrinsically required for post-transcriptional regulation of Drosophila Germline Stem Cell (GSC) maintenance. Sci Rep 2019; 9:4372. [PMID: 30867469 PMCID: PMC6416348 DOI: 10.1038/s41598-019-40152-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/07/2019] [Indexed: 01/05/2023] Open
Abstract
A very important open question in stem cells regulation is how the fine balance between GSCs self-renewal and differentiation is orchestrated at the molecular level. In the past several years much progress has been made in understanding the molecular mechanisms underlying intrinsic and extrinsic controls of GSC regulation but the complex gene regulatory networks that regulate stem cell behavior are only partially understood. HP1 is a dynamic epigenetic determinant mainly involved in heterochromatin formation, epigenetic gene silencing and telomere maintenance. Furthermore, recent studies have revealed the importance of HP1 in DNA repair, sister chromatid cohesion and, surprisingly, in positive regulation of gene expression. Here, we show that HP1 plays a crucial role in the control of GSC homeostasis in Drosophila. Our findings demonstrate that HP1 is required intrinsically to promote GSC self-renewal and progeny differentiation by directly stabilizing the transcripts of key genes involved in GSCs maintenance.
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97
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Saha P, Sowpati DT, Mishra RK. Epigenomic and genomic landscape of Drosophila melanogaster heterochromatic genes. Genomics 2019; 111:177-185. [DOI: 10.1016/j.ygeno.2018.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 01/21/2018] [Accepted: 02/04/2018] [Indexed: 01/05/2023]
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98
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Leopold K, Stirpe A, Schalch T. Transcriptional gene silencing requires dedicated interaction between HP1 protein Chp2 and chromatin remodeler Mit1. Genes Dev 2019; 33:565-577. [PMID: 30808655 PMCID: PMC6499331 DOI: 10.1101/gad.320440.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/05/2019] [Indexed: 11/25/2022]
Abstract
Heterochromatin protein 1 (HP1) proteins are key factors of eukaryotic heterochromatin that coordinate chromatin compaction and transcriptional gene silencing. Through their multivalency they act as adaptors between histone H3 Lys9 di/trimethyl marks in chromatin and effector complexes that bind to the HP1 chromoshadow domain. Most organisms encode for multiple HP1 isoforms and the molecular mechanisms that underpin their diverse functions in genome regulation remain poorly understood. In fission yeast, the two HP1 proteins Chp2 and Swi6 assume distinct roles and Chp2 is tightly associated with the nucleosome remodeling and deacetylation complex SHREC. Here we show that Chp2 directly engages the SHREC nucleosome remodeler subunit Mit1. The crystal structure of the interaction interface reveals an extraordinarily extensive and specific interaction between the chromoshadow domain of Chp2 and the N terminus of Mit1. The integrity of this interface is critical for high affinity binding and for heterochromatin formation. Comparison with Swi6 shows that the Chp2-Mit1 interface is highly selective and thereby provides the molecular basis for the functional specialization of an HP1 isoform.
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Affiliation(s)
- Karoline Leopold
- Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Alessandro Stirpe
- Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Thomas Schalch
- Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland.,Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, United Kingdom
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99
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Wilson C, Krieg AJ. KDM4B: A Nail for Every Hammer? Genes (Basel) 2019; 10:E134. [PMID: 30759871 PMCID: PMC6410163 DOI: 10.3390/genes10020134] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/05/2019] [Accepted: 02/07/2019] [Indexed: 01/01/2023] Open
Abstract
Epigenetic changes are well-established contributors to cancer progression and normal developmental processes. The reversible modification of histones plays a central role in regulating the nuclear processes of gene transcription, DNA replication, and DNA repair. The KDM4 family of Jumonj domain histone demethylases specifically target di- and tri-methylated lysine 9 on histone H3 (H3K9me3), removing a modification central to defining heterochromatin and gene repression. KDM4 enzymes are generally over-expressed in cancers, making them compelling targets for study and therapeutic inhibition. One of these family members, KDM4B, is especially interesting due to its regulation by multiple cellular stimuli, including DNA damage, steroid hormones, and hypoxia. In this review, we discuss what is known about the regulation of KDM4B in response to the cellular environment, and how this context-dependent expression may be translated into specific biological consequences in cancer and reproductive biology.
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Affiliation(s)
- Cailin Wilson
- Department of Pathology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239, USA.
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR 97006, USA.
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100
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Lee DH, Ryu HW, Kim GW, Kwon SH. Comparison of three heterochromatin protein 1 homologs in Drosophila. J Cell Sci 2019; 132:jcs.222729. [PMID: 30659116 DOI: 10.1242/jcs.222729] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/22/2018] [Indexed: 01/20/2023] Open
Abstract
Heterochromatin protein 1 (HP1) is an epigenetic regulator of chromatin structure and genome function in eukaryotes. Despite shared features, most eukaryotes have a minimum of three HP1 homologs with differential localization patterns and functions. Most studies focus on Drosophila HP1a [also known as Su(var)205], and little is known about the properties of HP1b and HP1c. To determine the features of the three HP1 homologs, we performed the first comprehensive comparative analysis of Drosophila HP1 homologs. HP1 differentially homodimerizes and heterodimerizes in vivo and in vitro HP1b and HP1c, but not HP1a, are localized to both the nucleus and cytoplasm. The C-terminal extension region (CTE) targets HP1c and HP1b to the cytoplasm. Biochemical approaches show that HP1 binds to various interacting partners with different binding affinities. Each HP1 associates differently with RNA polymerase II; a gene reporter assay revealed that HP1a and HP1b, but not HP1c, inhibit transcriptional activity, suggesting that HP1c serves as a positive regulator in transcription. Thus, these studies provide the basic clues pertaining to the molecular mechanism by which HP1 might control cellular processes in a homolog-specific manner.
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Affiliation(s)
- Dong Hoon Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyun Wook Ryu
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983, Republic of Korea .,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Republic of Korea
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