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Huan Q, Mao Z, Chong K, Zhang J. Global analysis of H3K4me3/H3K27me3 in Brachypodium distachyon reveals VRN3 as critical epigenetic regulation point in vernalization and provides insights into epigenetic memory. THE NEW PHYTOLOGIST 2018; 219:1373-1387. [PMID: 30063801 DOI: 10.1111/nph.15288] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 05/20/2018] [Indexed: 05/21/2023]
Abstract
Vernalization, the requirement of plants for long-term exposure to low environmental temperature for flowering, is an epigenetic phenomenon. Histone modification regulation has been revealed in vernalization, but is limited to key genes. Now, we know that VRN1 is epigenetically critical for monocots. Genome-wide analysis is still unavailable, however. We performed chromatin immunoprecipitation-sequencing for H3K4me3/H3K27me3 in Brachypodium distachyon to obtain a global view of histone modifications in vernalization on a genome-wide scale and for different pathways/genes. Our data showed that H3K4me3 and H3K27me3 play distinct roles in vernalization. Unlike H3K4me3, H3K27me3 exhibited regional regulation, showed main regulation targets in vernalization and contributed to epigenetic memory. For genes in four flowering regulation pathways, only FT2 (functional ortholog of VRN3 in B. distachyon) and VRN1 showed coordinated changes in H3K4me3/H3K27me3. The epigenetic response at VRN3 was weaker under short-day than under long-day conditions. VRN3 was revealed as an epigenetic regulation point integrating vernalization and day length signals. We globally identified genes maintaining vernalization-induced epigenetic changes. Most of these genes showed dose-dependent vernalization responses, revealing a quantitative 'recording system' for vernalization. Our studies shed light on the epigenetic role of VRN3 and H3K4me3/H3K27me3 in vernalization and reveal genes underlying epigenetic memory, laying the foundation for further study.
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Affiliation(s)
- Qing Huan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiwei Mao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jingyu Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Jiang Y, Liu Y, Lu H, Sun SC, Jin W, Wang X, Dong C. Epigenetic activation during T helper 17 cell differentiation is mediated by Tripartite motif containing 28. Nat Commun 2018; 9:1424. [PMID: 29651155 PMCID: PMC5897371 DOI: 10.1038/s41467-018-03852-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 03/14/2018] [Indexed: 12/02/2022] Open
Abstract
Epigenetic regulation is important for T-cell fate decision. Although STAT3 is known to initiate Th17 differentiation program, the downstream mechanism is unclear. Here we show that Tripartite motif containing 28 (Trim28) expression in Th17 cells is required for Th17-mediated cytokine production and experimental autoimmune diseases. Genome-wide occupancy analysis reveals that TRIM28-bound regions overlap with almost all Th17-specific super-enhancers (SE), and that those SEs are impaired by the deficiency of STAT3 or TRIM28, but not of RORγt. Importantly, IL-6-STAT3 signaling facilitates TRIM28 binding to the Il17-Il17f locus, and this process is required for epigenetic activation and high-order chromosomal interaction. TRIM28 also forms a complex with STAT3 and RORγt, and promotes the recruitment of RORγt to its target cytokine genes. Our study thus suggests TRIM28 to be important for the epigenetic activation during Th17 cell differentiation, and prompts the potential use of epigenetic interventions for Th17-related autoimmune diseases. T help 17 (Th17) cells are important mediators for both protective and pathogenic immune reactions, but how their functions are regulated at the epigenetic level is not understood. Here the authors show that TRIM28, a cofactor for transcriptional regulation, is important for epigenetic activation of Th17-related gene loci during Th17 response.
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Affiliation(s)
- Yu Jiang
- Institute for Immunology and School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Ying Liu
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Huiping Lu
- Institute for Immunology and School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Shao-Cong Sun
- Department of Immunology and Center for Inflammation and Cancer, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wei Jin
- Institute for Immunology and School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Xiaohu Wang
- Institute for Immunology and School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Chen Dong
- Institute for Immunology and School of Medicine, Tsinghua University, 100084, Beijing, China. .,Beijing Key Lab for Immunological Research on Chronic Diseases, 100084, Beijing, China.
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Carucci N, Cacci E, Nisi PS, Licursi V, Paul YL, Biagioni S, Negri R, Rugg-Gunn PJ, Lupo G. Transcriptional response of Hoxb genes to retinoid signalling is regionally restricted along the neural tube rostrocaudal axis. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160913. [PMID: 28484611 PMCID: PMC5414248 DOI: 10.1098/rsos.160913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/07/2017] [Indexed: 06/07/2023]
Abstract
During vertebrate neural development, positional information is largely specified by extracellular morphogens. Their distribution, however, is very dynamic due to the multiple roles played by the same signals in the developing and adult neural tissue. This suggests that neural progenitors are able to modify their competence to respond to morphogen signalling and autonomously maintain positional identities after their initial specification. In this work, we take advantage of in vitro culture systems of mouse neural stem/progenitor cells (NSPCs) to show that NSPCs isolated from rostral or caudal regions of the mouse neural tube are differentially responsive to retinoic acid (RA), a pivotal morphogen for the specification of posterior neural fates. Hoxb genes are among the best known RA direct targets in the neural tissue, yet we found that RA could promote their transcription only in caudal but not in rostral NSPCs. Correlating with these effects, key RA-responsive regulatory regions in the Hoxb cluster displayed opposite enrichment of activating or repressing histone marks in rostral and caudal NSPCs. Finally, RA was able to strengthen Hoxb chromatin activation in caudal NSPCs, but was ineffective on the repressed Hoxb chromatin of rostral NSPCs. These results suggest that the response of NSPCs to morphogen signalling across the rostrocaudal axis of the neural tube may be gated by the epigenetic configuration of target patterning genes, allowing long-term maintenance of intrinsic positional values in spite of continuously changing extrinsic signals.
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Affiliation(s)
- Nicoletta Carucci
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Emanuele Cacci
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Paola S. Nisi
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Yu-Lee Paul
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Stefano Biagioni
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology ‘C. Darwin’, Sapienza University of Rome, 00185 Rome, Italy
- Istituto Pasteur— Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Giuseppe Lupo
- Istituto Pasteur— Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy
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Kalyani R, Lee JY, Min H, Yoon H, Kim MH. Genes Frequently Coexpressed with Hoxc8 Provide Insight into the Discovery of Target Genes. Mol Cells 2016; 39:395-402. [PMID: 27025388 PMCID: PMC4870187 DOI: 10.14348/molcells.2016.2311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/05/2016] [Accepted: 02/15/2016] [Indexed: 12/12/2022] Open
Abstract
Identifying Hoxc8 target genes is at the crux of understanding the Hoxc8-mediated regulatory networks underlying its roles during development. However, identification of these genes remains difficult due to intrinsic factors of Hoxc8, such as low DNA binding specificity, context-dependent regulation, and unknown cofactors. Therefore, as an alternative, the present study attempted to test whether the roles of Hoxc8 could be inferred by simply analyzing genes frequently coexpressed with Hoxc8, and whether these genes include putative target genes. Using archived gene expression datasets in which Hoxc8 was differentially expressed, we identified a total of 567 genes that were positively coexpressed with Hoxc8 in at least four out of eight datasets. Among these, 23 genes were coexpressed in six datasets. Gene sets associated with extracellular matrix and cell adhesion were most significantly enriched, followed by gene sets for skeletal system development, morphogenesis, cell motility, and transcriptional regulation. In particular, transcriptional regulators, including paralogs of Hoxc8, known Hox co-factors, and transcriptional remodeling factors were enriched. We randomly selected Adam19, Ptpn13, Prkd1, Tgfbi, and Aldh1a3, and validated their coexpression in mouse embryonic tissues and cell lines following TGF-β2 treatment or ectopic Hoxc8 expression. Except for Aldh1a3, all genes showed concordant expression with that of Hoxc8, suggesting that the coexpressed genes might include direct or indirect target genes. Collectively, we suggest that the coexpressed genes provide a resource for constructing Hoxc8-mediated regulatory networks.
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Affiliation(s)
- Ruthala Kalyani
- Department of Anatomy, Embryology Lab., Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722,
Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Lab., Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722,
Korea
| | - Hyehyun Min
- Department of Anatomy, Embryology Lab., Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722,
Korea
| | - Heejei Yoon
- Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Seoul 06351,
Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Lab., Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722,
Korea
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Min H, Kong KA, Lee JY, Hong CP, Seo SH, Roh TY, Bae SS, Kim MH. CTCF-mediated Chromatin Loop for the Posterior Hoxc Gene Expression in MEF Cells. IUBMB Life 2016; 68:436-44. [PMID: 27080371 DOI: 10.1002/iub.1504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/15/2016] [Accepted: 03/25/2016] [Indexed: 01/06/2023]
Abstract
Modulation of chromatin structure has been proposed as a molecular mechanism underlying the spatiotemporal collinear expression of Hox genes during development. CCCTC-binding factor (CTCF)-mediated chromatin organization is now recognized as a crucial epigenetic mechanism for transcriptional regulation. Thus, we examined whether CTCF-mediated chromosomal conformation is involved in Hoxc gene expression by comparing wild-type mouse embryonic fibroblast (MEF) cells expressing anterior Hoxc genes with Akt1 null MEFs expressing anterior as well as posterior Hoxc genes. We found that CTCF binding between Hoxc11 and -c12 is important for CTCF-mediated chromosomal loop formation and concomitant posterior Hoxc gene expression. Hypomethylation at this site increased CTCF binding and recapitulated the chromosomal conformation and posterior Hoxc gene expression patterns observed in Akt1 null MEFs. From this work we found that CTCF at the C12|11 does not function as a barrier/boundary, instead let the posterior Hoxc genes switch their interaction from inactive centromeric to active telomeric genomic niche, and concomitant posterior Hoxc gene expression. Although it is not clear whether CTCF affects Hoxc gene expression solely through its looping activity, CTCF-mediated chromatin structural modulation could be an another tier of Hox gene regulation during development. © 2016 IUBMB Life, 68(6):436-444, 2016.
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Affiliation(s)
- Hyehyun Min
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyoung-Ah Kong
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Chang-Pyo Hong
- Department of Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Seong-Hye Seo
- Department of Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Sun Sik Bae
- Department of Pharmacology, MRC For Ischemic Tissue Regeneration, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
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Yang M, Youn JI, Kim SJ, Park JY. Epigenetic modulation of Chlorella (Chlorella vulgaris) on exposure to polycyclic aromatic hydrocarbons. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2015; 40:758-763. [PMID: 26432772 DOI: 10.1016/j.etap.2015.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 09/04/2015] [Accepted: 09/07/2015] [Indexed: 06/05/2023]
Abstract
DNA methylation in promoter region can be a new chemopreventive marker against polycyclic aromatic hydrocarbons (PAHs). We performed a randomized, double blind and cross-over trial (N=12 healthy females) to evaluate chlorella (Chlorella vulgaris)-induced epigenetic modulation on exposure to PAHs. The subjects consumed 4 tablets of placebo or chlorella supplement (total chlorophyll ≈ 8.3mg/tablet) three times a day before meals for 2 weeks. When the subjects consumed chlorella, status of global hypermethylation (5-methylcytosine) was reduced, compared to placebo (p=0.04). However, DNA methylation at the DNMT1 or NQO1 was not modified by chlorella. We observed the reduced levels of urinary 1-hydroxypyrene (1-OHP), a typical metabolite of PAHs, by chlorella intake (p<0.1) and a positive association between chlorella-induced changes in global hypermethylation and urinary 1-OHP (p<0.01). Therefore, our study suggests chlorella works for PAH-detoxification through the epigenetic modulation, the interference of ADME of PAHs and the interaction of mechanisms.
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Affiliation(s)
- Mihi Yang
- College of Pharmacy, Sookmyoung Women's University, Seoul, Republic of Korea.
| | - Je-In Youn
- Wide River Institute of Immunology, Department of Biomedical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Seung Joon Kim
- Division of Pulmonology, Department of Internal Medicine, the Catholic University of Korea, Seoul, Republic of Korea
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
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Kong KA, Lee JY, Oh JH, Lee Y, Kim MH. Akt1 mediates the posterior Hoxc gene expression through epigenetic modifications in mouse embryonic fibroblasts. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:793-9. [PMID: 24955524 DOI: 10.1016/j.bbagrm.2014.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 05/09/2014] [Accepted: 06/11/2014] [Indexed: 12/20/2022]
Abstract
The evolutionarily conserved Hox genes are organized in clusters and expressed colinearly to specify body patterning during embryonic development. Previously, Akt1 has been identified as a putative Hox gene regulator through in silico analysis. Substantial upregulation of consecutive 5' Hoxc genes has been observed when Akt1 is absent in mouse embryonic fibroblast (MEF) cells. In this study, we provide evidence that Akt1 regulates the 5' Hoxc gene expression by epigenetic modifications. Enrichment of histone H3K9 acetylation and a low level of the H3K27me3 mark were detected at the posterior 5' Hoxc loci when Akt1 is absent. A histone deacetylase (HDAC) inhibitor de-repressed 5' Hoxc gene expression when Akt1 is present, and a DNA demethylating reagent synergistically upregulated HDAC-induced 5' Hoxc gene expression. A knockdown study revealed that Hdac6 is mediated in the Hoxc12 repression through direct binding to the transcription start site (TSS) in the presence of Akt1. Co-immunoprecipitation analysis revealed that endogenous Akt1 directly interacted with Hdac6. Furthermore, exogenous Akt1 was enriched at the promoter region of the posterior Hoxc genes such as Hoxc11 and Hoxc12, not the Akt1-independent Hoxc5 and Hoxd10 loci. The regulation of the H3K27me3 mark by Ezh2 and Kdm6b at the 5' Hoxc gene promoter turned out to be Akt1 dependent. Taken together, these results suggest that Akt1 mediates the posterior 5' Hoxc gene expression through epigenetic modification such as histone methylation and acetylation, and partly through a direct binding to the promoter region of the 5' Hoxc genes and/or Hdac6 in mouse embryonic fibroblast cells.
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Affiliation(s)
- Kyoung-Ah Kong
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji Hoon Oh
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Youra Lee
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Lab., Yonsei University College of Medicine, Seoul, Republic of Korea.
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Min H, Lee JY, Kim MH. Hoxc gene collinear expression and epigenetic modifications established during embryogenesis are maintained until after birth. Int J Biol Sci 2013; 9:960-5. [PMID: 24155669 PMCID: PMC3805901 DOI: 10.7150/ijbs.6739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/12/2013] [Indexed: 11/05/2022] Open
Abstract
The Hox genes, which are organized into clusters on different chromosomes, are key regulators of embryonic anterior-posterior (A-P) body pattern formation and are expressed at specific times and in specific positions in developing vertebrate embryos. Previously, we have shown that histone methylation patterns are closely correlated with collinear Hox gene expression patterns along the A-P axis of E14.5 mouse embryos. Since histone modification is thought to play a crucial mechanistic role in the highly coordinated pattern of collinear Hox gene expression, we examined the maintenance of the spatial collinear expression pattern of Hoxc genes and the corresponding histone modifications during embryogenesis and in early postnatal mice. Hox expression patterns and histone modifications were analyzed by semi-quantitative RT-PCR and chromatin immunoprecipitation (ChIP)-PCR analyses, respectively. The spatiotemporal expression patterns of Hoxc genes in a cluster were maintained until the early postnatal stage (from E8.5 through P5). Examination of histone modifications in E14.5 and P5 tissues revealed that level of H3K27me3 is only a weak correlation with collinear Hoxc gene expression in the trunk regions although diminished in general, however the enrichment of H3K4me3 is strongly correlated with the gene expression in both stages. In summary, the initial spatiotemporal collinear expression pattern of Hoxc genes and epigenetic modifications are maintained after birth, likely contributing to the establishment of the gene expression code for position in the anatomic body axis throughout the entire life of the organism.
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Affiliation(s)
- Hyehyun Min
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Korea
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