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Hsu E, Hutchison K, Liu Y, Nicolet CM, Schreiner S, Zemke N, Farnham P. Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters. Nucleic Acids Res 2024; 52:6850-6865. [PMID: 38726870 PMCID: PMC11229363 DOI: 10.1093/nar/gkae372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 07/09/2024] Open
Abstract
The ZFX transcriptional activator binds to CpG island promoters, with a major peak at ∼200-250 bp downstream from transcription start sites. Because ZFX binds within the transcribed region, we investigated whether it regulates transcriptional elongation. We used GRO-seq to show that loss or reduction of ZFX increased Pol2 pausing at ZFX-regulated promoters. To further investigate the mechanisms by which ZFX regulates transcription, we determined regions of the protein needed for transactivation and for recruitment to the chromatin. Interestingly, although ZFX has 13 grouped zinc fingers, deletion of the first 11 fingers produces a protein that can still bind to chromatin and activate transcription. We next used TurboID-MS to detect ZFX-interacting proteins, identifying ZNF593, as well as proteins that interact with the N-terminal transactivation domain (which included histone modifying proteins), and proteins that interact with ZFX when it is bound to the chromatin (which included TAFs and other histone modifying proteins). Our studies support a model in which ZFX enhances elongation at target promoters by recruiting H4 acetylation complexes and reducing pausing.
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Affiliation(s)
- Emily Hsu
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Katherine Hutchison
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Yao Liu
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Charles M Nicolet
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Shannon Schreiner
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Nathan R Zemke
- Department of Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, CA 92093, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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Zhao T, Hong Y, Yan B, Huang S, Ming GL, Song H. Epigenetic maintenance of adult neural stem cell quiescence in the mouse hippocampus via Setd1a. Nat Commun 2024; 15:5674. [PMID: 38971831 PMCID: PMC11227589 DOI: 10.1038/s41467-024-50010-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/25/2024] [Indexed: 07/08/2024] Open
Abstract
Quiescence, a hallmark of adult neural stem cells (NSCs), is required for maintaining the NSC pool to support life-long continuous neurogenesis in the adult dentate gyrus (DG). Whether long-lasting epigenetic modifications maintain NSC quiescence over the long term in the adult DG is not well-understood. Here we show that mice with haploinsufficiency of Setd1a, a schizophrenia risk gene encoding a histone H3K4 methyltransferase, develop an enlarged DG with more dentate granule cells after young adulthood. Deletion of Setd1a specifically in quiescent NSCs in the adult DG promotes their activation and neurogenesis, which is countered by inhibition of the histone demethylase LSD1. Mechanistically, RNA-sequencing and CUT & RUN analyses of cultured quiescent adult NSCs reveal Setd1a deletion-induced transcriptional changes and many Setd1a targets, among which down-regulation of Bhlhe40 promotes quiescent NSC activation in the adult DG in vivo. Together, our study reveals a Setd1a-dependent epigenetic mechanism that sustains NSC quiescence in the adult DG.
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Affiliation(s)
- Ting Zhao
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA
| | - Yan Hong
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA
| | - Bowen Yan
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Suming Huang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Oliviero G, Wynne K, Andrews D, Crean J, Kolch W, Cagney G. Expression Proteomics and Histone Analysis Reveal Extensive Chromatin Network Changes and a Role for Histone Tail Trimming during Cellular Differentiation. Biomolecules 2024; 14:747. [PMID: 39062462 PMCID: PMC11274982 DOI: 10.3390/biom14070747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
In order to understand the coordinated proteome changes associated with differentiation of a cultured cell pluripotency model, protein expression changes induced by treatment of NT2 embryonal carcinoma cells with retinoic acid were monitored by mass spectrometry. The relative levels of over 5000 proteins were mapped across distinct cell fractions. Analysis of the chromatin fraction revealed major abundance changes among chromatin proteins and epigenetic pathways between the pluripotent and differentiated states. Protein complexes associated with epigenetic regulation of gene expression, chromatin remodelling (e.g., SWI/SNF, NuRD) and histone-modifying enzymes (e.g., Polycomb, MLL) were found to be extensively regulated. We therefore investigated histone modifications before and after differentiation, observing changes in the global levels of lysine acetylation and methylation across the four canonical histone protein families, as well as among variant histones. We identified the set of proteins with affinity to peptides housing the histone marks H3K4me3 and H3K27me3, and found increased levels of chromatin-associated histone H3 tail trimming following differentiation that correlated with increased expression levels of cathepsin proteases. We further found that inhibition of cathepsins B and D reduces histone H3 clipping. Overall, the work reveals a global reorganization of the cell proteome congruent with differentiation, highlighting the key role of multiple epigenetic pathways, and demonstrating a direct link between cathepsin B and D activity and histone modification.
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Affiliation(s)
- Giorgio Oliviero
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (K.W.); (W.K.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
- School of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (K.W.); (W.K.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
| | - Darrell Andrews
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
| | - John Crean
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
- School of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland; (K.W.); (W.K.)
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
| | - Gerard Cagney
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland; (D.A.); (J.C.)
- School of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland
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Kang J, Kang Y, Kim A. Histone H3K4ac, as a marker of active transcription start sites and enhancers, plays roles in histone eviction and RNA transcription. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195021. [PMID: 38417480 DOI: 10.1016/j.bbagrm.2024.195021] [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: 11/27/2023] [Revised: 02/01/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
The lysine 4 of histone H3 (H3K4) can be methylated or acetylated into four states: H3K4me1, H3K4me2, H3K4me3, or H3K4ac. Unlike H3K4 methylation, the genome-wide distribution and functional roles of H3K4ac remain unclear. To understand the relationship of acetylation with methylation at H3K4 and to explore the roles of H3K4ac in the context of chromatin, we analyzed H3K4ac across the human genome and compared it with H3K4 methylation in K562 cells. H3K4ac was positively correlated with H3K4me1/2/3 in reciprocal analysis. A decrease in H3K4ac through the mutation of the histone acetyltransferase p300 reduced H3K4me1 and H3K4me3 at the H3K4ac peaks. H3K4ac was also impaired by H3K4me depletion in the histone methyltransferase MLL3/4-mutated cells. H3K4ac peaks were enriched at enhancers in addition to the transcription start sites (TSSs) of genes. H3K4ac of TSSs and enhancers was positively correlated with mRNA and eRNA transcription. A decrease in H3K4ac reduced H3K4me3 and H3K4me1 in TSSs and enhancers, respectively, and inhibited the eviction of histone H3 from them. The mRNA transcription of highly transcribed genes was affected by the reduced H3K4ac. Interestingly, H3K4ac played a redundant role with regard to H3K27ac in eRNA transcription. These results indicate that H3K4ac serves as a marker of both active TSSs and enhancers and plays a role in histone eviction and RNA transcription by leading to H3K4me1/3.
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Affiliation(s)
- Jin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Yujin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - AeRi Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea.
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5
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Bittel AJ, Chen YW. DNA Methylation in the Adaptive Response to Exercise. Sports Med 2024; 54:1419-1458. [PMID: 38561436 DOI: 10.1007/s40279-024-02011-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
Emerging evidence published over the past decade has highlighted the role of DNA methylation in skeletal muscle function and health, including as an epigenetic transducer of the adaptive response to exercise. In this review, we aim to synthesize the latest findings in this field to highlight: (1) the shifting understanding of the genomic localization of altered DNA methylation in response to acute and chronic aerobic and resistance exercise in skeletal muscle (e.g., promoter, gene bodies, enhancers, intergenic regions, un-annotated regions, and genome-wide methylation); (2) how these global/regional methylation changes relate to transcriptional activity following exercise; and (3) the factors (e.g., individual demographic or genetic features, dietary, training history, exercise parameters, local epigenetic characteristics, circulating hormones) demonstrated to alter both the pattern of DNA methylation after exercise, and the relationship between DNA methylation and gene expression. Finally, we discuss the changes in non-CpG methylation and 5-hydroxymethylation after exercise, as well as the importance of emerging single-cell analyses to future studies-areas of increasing focus in the field of epigenetics. We anticipate that this review will help generate a framework for clinicians and researchers to begin developing and testing exercise interventions designed to generate targeted changes in DNA methylation as part of a personalized exercise regimen.
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Affiliation(s)
- Adam J Bittel
- Research Center for Genetic Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA.
| | - Yi-Wen Chen
- Research Center for Genetic Medicine, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Science, 111 Michigan Ave NW, Washington, DC, 20010, USA
- Department of Integrative Systems Biology, Institute for Biomedical Sciences, The George Washington University, 2121 I St NW, Washington, DC, 20052, USA
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6
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Ren L, Ma W, Wang Y. Predicting RNA polymerase II transcriptional elongation pausing and associated histone code. Brief Bioinform 2024; 25:bbae246. [PMID: 38783706 PMCID: PMC11116834 DOI: 10.1093/bib/bbae246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/12/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
RNA Polymerase II (Pol II) transcriptional elongation pausing is an integral part of the dynamic regulation of gene transcription in the genome of metazoans. It plays a pivotal role in many vital biological processes and disease progression. However, experimentally measuring genome-wide Pol II pausing is technically challenging and the precise governing mechanism underlying this process is not fully understood. Here, we develop RP3 (RNA Polymerase II Pausing Prediction), a network regularized logistic regression machine learning method, to predict Pol II pausing events by integrating genome sequence, histone modification, gene expression, chromatin accessibility, and protein-protein interaction data. RP3 can accurately predict Pol II pausing in diverse cellular contexts and unveil the transcription factors that are associated with the Pol II pausing machinery. Furthermore, we utilize a forward feature selection framework to systematically identify the combination of histone modification signals associated with Pol II pausing. RP3 is freely available at https://github.com/AMSSwanglab/RP3.
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Affiliation(s)
- Lixin Ren
- School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Wanbiao Ma
- School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, 55 Zhongguancun East Road, Haidian District, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Wuhua District, Kunming 650223, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 1 Xiangshan Zhi Nong, West Lake District, Hangzhou 330106, China
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7
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Giaimo BD, Friedrich T, Ferrante F, Bartkuhn M, Borggrefe T. Comprehensive genomic features indicative for Notch responsiveness. Nucleic Acids Res 2024; 52:5179-5194. [PMID: 38647081 PMCID: PMC11109962 DOI: 10.1093/nar/gkae292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Transcription factor RBPJ is the central component in Notch signal transduction and directly forms a coactivator complex together with the Notch intracellular domain (NICD). While RBPJ protein levels remain constant in most tissues, dynamic expression of Notch target genes varies depending on the given cell-type and the Notch activity state. To elucidate dynamic RBPJ binding genome-wide, we investigated RBPJ occupancy by ChIP-Seq. Surprisingly, only a small set of the total RBPJ sites show a dynamic binding behavior in response to Notch signaling. Compared to static RBPJ sites, dynamic sites differ in regard to their chromatin state, binding strength and enhancer positioning. Dynamic RBPJ sites are predominantly located distal to transcriptional start sites (TSSs), while most static sites are found in promoter-proximal regions. Importantly, gene responsiveness is preferentially associated with dynamic RBPJ binding sites and this static and dynamic binding behavior is repeatedly observed across different cell types and species. Based on the above findings we used a machine-learning algorithm to predict Notch responsiveness with high confidence in different cellular contexts. Our results strongly support the notion that the combination of binding strength and enhancer positioning are indicative of Notch responsiveness.
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Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Tobias Friedrich
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University Giessen, Aulweg 128, 35392 Giessen, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University Giessen, Aulweg 128, 35392 Giessen, Germany
- Institute for Lung Health, Aulweg 132, 35392 Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
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8
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Chaowongdee S, Vannatim N, Malichan S, Kuncharoen N, Tongyoo P, Siriwan W. Comparative transcriptomics analysis reveals defense mechanisms of Manihot esculenta Crantz against Sri Lanka Cassava MosaicVirus. BMC Genomics 2024; 25:436. [PMID: 38698332 PMCID: PMC11067156 DOI: 10.1186/s12864-024-10315-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Cassava mosaic disease (CMD), caused by Sri Lankan cassava mosaic virus (SLCMV) infection, has been identified as a major pernicious disease in Manihot esculenta Crantz (cassava) plantations. It is widespread in Southeast Asia, especially in Thailand, which is one of the main cassava supplier countries. With the aim of restricting the spread of SLCMV, we explored the gene expression of a tolerant cassava cultivar vs. a susceptible cassava cultivar from the perspective of transcriptional regulation and the mechanisms underlying plant immunity and adaptation. RESULTS Transcriptomic analysis of SLCMV-infected tolerant (Kasetsart 50 [KU 50]) and susceptible (Rayong 11 [R 11]) cultivars at three infection stages-that is, at 21 days post-inoculation (dpi) (early/asymptomatic), 32 dpi (middle/recovery), and 67 dpi (late infection/late recovery)-identified 55,699 expressed genes. Differentially expressed genes (DEGs) between SLCMV-infected KU 50 and R 11 cultivars at (i) 21 dpi to 32 dpi (the early to middle stage), and (ii) 32 dpi to 67 dpi (the middle stage to late stage) were then identified and validated by real-time quantitative PCR (RT-qPCR). DEGs among different infection stages represent genes that respond to and regulate the viral infection during specific stages. The transcriptomic comparison between the tolerant and susceptible cultivars highlighted the role of gene expression regulation in tolerant and susceptible phenotypes. CONCLUSIONS This study identified genes involved in epigenetic modification, transcription and transcription factor activities, plant defense and oxidative stress response, gene expression, hormone- and metabolite-related pathways, and translation and translational initiation activities, particularly in KU 50 which represented the tolerant cultivar in this study.
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Affiliation(s)
- Somruthai Chaowongdee
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok, 10900, Thailand
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand
| | - Nattachai Vannatim
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Srihunsa Malichan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Nattakorn Kuncharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Pumipat Tongyoo
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok, 10900, Thailand
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand
| | - Wanwisa Siriwan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand.
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Rehman S, Storey KB. Dynamics of epigenetic regulation in Dryophytes versicolor skeletal muscle: Lysine methylation and acetylation involvement in metabolic rate depression. J Therm Biol 2024; 122:103865. [PMID: 38761482 DOI: 10.1016/j.jtherbio.2024.103865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/20/2024]
Abstract
For the breadth of the winter, Dryophytes versicolor can survive full body freezing utilizing a phenomenon known as metabolic rate depression (MRD). Epigenetic transcriptional control on gene expression, such as histone methylation and acetylation, can aid in implementing a balance between permissive and restricted chromatin required to endure this stress. As such, this study explores the interplay between histone lysine methyl and acetyl transferases (HKMTs, HATs), as well as the abundance of various acetyl-lysine and methyl-lysine moieties on histone H3 and H4. Results showing that overexpression of transcriptionally repressive marks, and under expression of active ones, suggest a negative effect on overall gene transcription in skeletal muscle tissue.
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Affiliation(s)
- Saif Rehman
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Kenneth B Storey
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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10
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Qiu X, Zhang S, Zhang Y, Cai L, Li D, Lu Y. Reduction of ETV1 is Identified as a Prominent Feature of Age-Related Cataract. Curr Eye Res 2024; 49:496-504. [PMID: 38200696 DOI: 10.1080/02713683.2024.2302545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 01/01/2024] [Indexed: 01/12/2024]
Abstract
PURPOSE To identify the inactive genes in cataract lenses and explore their function in lens epithelial cells (LECs). METHODS Lens epithelium samples obtained from both age-related cataract (ARC) patients and normal donors were subjected to two forms of histone H3 immunoprecipitation: H3K9ac and H3K27me3 chromatin immunoprecipitation (ChIP), followed by ChIP-seq. The intersection set of "active genes in normal controls" and "repressed genes in cataract lenses" was identified. To validate the role of a specific gene, ETV1, within this set, quantitative polymerase chain reaction (qPCR), western blot, and immunofluorescence were performed using clinical lens epithelium samples. Small interference RNA (siRNA) was utilized to reduce the mRNA level of ETV1 in cultured LECs. Following this, transwell assay and western blot was performed to examine the migration ability of the cells. Furthermore, RNA-seq analysis was conducted on both cell samples with ETV1 knockdown and control cells. Additionally, the expression level of ETV1 in LECs was examined using qPCR under H2O2 treatment. RESULTS Six genes were identified in the intersection set of "active genes in normal controls" and "repressed genes in ARC lenses". Among these genes, ETV1 showed the most significant fold-change decrease in the cataract samples compared to the control samples. After ETV1 knockdown by siRNA in cultured LECs, reduced cell migration was observed, along with a decrease in the expression of β-Catenin and Vimentin, two specific genes associated with cell migration. In addition, under the oxidative stress induced by H2O2 treatment, the expression level of ETV1 in LECs significantly decreased. CONCLUSIONS Based on the findings of this study, it can be concluded that ETV1 is significantly reduced in human ARC lenses. The repression of ETV1 in ARC lenses appears to contribute to the disrupted differentiation of lens epithelium, which is likely caused by the inhibition of both cell differentiation and migration processes.
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Affiliation(s)
- Xiaodi Qiu
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Shaohua Zhang
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Youmeng Zhang
- Department of Stomatology, Eye & ENT Hospital of Fudan University, Shanghai, China
| | - Lei Cai
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Dan Li
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yi Lu
- Eye Institute, Eye & ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
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11
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Li J, Gu W, Yang Z, Chen J, Yi F, Li T, Li J, Zhou Y, Guo Y, Song W, Lai J, Zhao H. ZmELP1, an Elongator complex subunit, is required for the maintenance of histone acetylation and RNA Pol II phosphorylation in maize kernels. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1251-1268. [PMID: 38098341 PMCID: PMC11022810 DOI: 10.1111/pbi.14262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 01/26/2024]
Abstract
The Elongator complex was originally identified as an interactor of hyperphosphorylated RNA polymerase II (RNAPII) in yeast and has histone acetyltransferase (HAT) activity. However, the genome-wide regulatory roles of Elongator on transcriptional elongation and histone acetylation remain unclear. We characterized a maize miniature seed mutant, mn7 and map-based cloning revealed that Mn7 encodes one of the subunits of the Elongator complex, ZmELP1. ZmELP1 deficiency causes marked reductions in the kernel size and weight. Molecular analyses showed that ZmELP1 interacts with ZmELP3, which is required for H3K14 acetylation (H3K14ac), and Elongator complex subunits interact with RNA polymerase II (RNAPII) C-terminal domain (CTD). Genome-wide analyses indicated that loss of ZmELP1 leads to a significant decrease in the deposition of H3K14ac and the CTD of phosphorylated RNAPII on Ser2 (Ser2P). These chromatin changes positively correlate with global transcriptomic changes. ZmELP1 mutation alters the expression of genes involved in transcriptional regulation and kernel development. We also showed that the decrease of Ser2P depends on the deposition of Elongator complex-mediated H3K14ac. Taken together, our results reveal an important role of ZmELP1 in the H3K14ac-dependent transcriptional elongation, which is critical for kernel development.
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Affiliation(s)
- Jianrui Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Wei Gu
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Crop Breeding, Cultivation Research Institution/CIMMYT‐China Specialty Maize Research Center, Shanghai Engineering Research Center of Specialty Maize, Shanghai Key Laboratory of Agricultural Genetics and BreedingShanghai Academy of Agricultural SciencesShanghaiChina
| | - Zhijia Yang
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jian Chen
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Fei Yi
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Tong Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jingrui Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Weibin Song
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Haiming Zhao
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
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Emerson J, Delgado T, Hong M, Keillor JW, Johnson GVW. Stabilizing transglutaminase 2 in the open conformation results in reactive astrocytes being more neurosupportive. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589192. [PMID: 38659783 PMCID: PMC11042235 DOI: 10.1101/2024.04.15.589192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Astrocytes play critical roles in supporting structural and metabolic homeostasis in the central nervous system (CNS). Inflammatory conditions bring about a range of poorly understood, heterogeneous, reactive phenotypes in astrocytes. Finding ways to manipulate the phenotype of reactive astrocytes, and leveraging a pro-recovery phenotype, holds promise in treating CNS injury. Previous studies have shown that the protein transglutaminase 2 (TG2) plays a significant role in determining the phenotype of reactive astrocytes. Recently it has been demonstrated that ablation of TG2 from astrocytes improves injury outcomes both in vitro and in vivo. Excitingly, in an in vivo mouse model, pharmacological inhibition of TG2 with the irreversible inhibitor VA4 phenocopies the neurosupportive effects of TG2 deletion in astrocytes. The focus of this study was to provide insights into the mechanisms by which TG2 deletion or inhibition of TG2 with VA4 result in a more neurosupportive astrocytic phenotype. Using a neuron-astrocyte co-culture model of neurite outgrowth, we show that VA4 treatment improves the ability of astrocytes to support neurite outgrowth on an injury-relevant matrix, further validating the ability of VA4 to phenocopy astrocytic TG2 deletion. VA4 treatment of neurons alone had no effect on neurite outgrowth. VA4 covalently binds to active site residues of TG2 that are exposed in its open conformation and are critical for its enzymatic function, and prevents TG2 from taking on a closed conformation, which interferes with its protein scaffolding function. To begin to understand how pharmacologically altering TG2's conformation affects its ability to regulate reactive astrocyte phenotypes, we assayed the impact of VA4 on TG2's interaction with Zbtb7a, a transcription factor that we have previously identified as a TG2 interactor, and whose functional outputs are significantly regulated by TG2. The results of these studies demonstrated that VA4 significantly decreases the interaction of TG2 and Zbtb7a. Further, previous findings indicate that TG2 may act as an epigenetic regulator, through its nuclear protein-protein interactions, to modulate gene expression. Since both TG2 and Zbtb7a interact with members of the Sin3a chromatin repressor complex, we assayed the effect of TG2 deletion and VA4 treatment on histone acetylation and found significantly greater acetylation with TG2 deletion or inhibition with VA4. Overall, this work points toward a possible epigenetic mechanism by which genetic deletion or acute inhibition of TG2 leads to enhanced astrocytic support of neurons.
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Affiliation(s)
- Jacen Emerson
- 601 Elmwood Ave, box 604, Department of Anesthesiology and Perioperative Medicine, University of Rochester, Rochester, NY, 14620, USA
| | - Thomas Delgado
- 601 Elmwood Ave, box 604, Department of Anesthesiology and Perioperative Medicine, University of Rochester, Rochester, NY, 14620, USA
| | - Matthew Hong
- 601 Elmwood Ave, box 604, Department of Anesthesiology and Perioperative Medicine, University of Rochester, Rochester, NY, 14620, USA
| | - Jeffrey W. Keillor
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N6N5, Canada
| | - Gail VW Johnson
- 601 Elmwood Ave, box 604, Department of Anesthesiology and Perioperative Medicine, University of Rochester, Rochester, NY, 14620, USA
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13
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Khatua P, Tang PK, Moulick AG, Patel R, Manandhar A, Loverde SM. Sequence Dependence in Nucleosome Dynamics. J Phys Chem B 2024; 128:3090-3101. [PMID: 38530903 PMCID: PMC11181342 DOI: 10.1021/acs.jpcb.3c07363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The basic packaging unit of eukaryotic chromatin is the nucleosome that contains 145-147 base pair duplex DNA wrapped around an octameric histone protein. While the DNA sequence plays a crucial role in controlling the positioning of the nucleosome, the molecular details behind the interplay between DNA sequence and nucleosome dynamics remain relatively unexplored. This study analyzes this interplay in detail by performing all-atom molecular dynamics simulations of nucleosomes, comparing the human α-satellite palindromic (ASP) and the strong positioning "Widom-601" DNA sequence at time scales of 12 μs. The simulations are performed at salt concentrations 10-20 times higher than physiological salt concentrations to screen the electrostatic interactions and promote unwrapping. These microsecond-long simulations give insight into the molecular-level sequence-dependent events that dictate the pathway of DNA unwrapping. We find that the "ASP" sequence forms a loop around SHL ± 5 for three sets of simulations. Coincident with loop formation is a cooperative increase in contacts with the neighboring N-terminal H2B tail and C-terminal H2A tail and the release of neighboring counterions. We find that the Widom-601 sequence exhibits a strong breathing motion of the nucleic acid ends. Coincident with the breathing motion is the collapse of the full N-terminal H3 tail and formation of an α-helix that interacts with the H3 histone core. We postulate that the dynamics of these histone tails and their modification with post-translational modifications (PTMs) may play a key role in governing this dynamics.
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Affiliation(s)
- Prabir Khatua
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- Present Address: Department of Chemistry, GITAM School of Science, GITAM (Deemed to be University), Bengaluru, 562163, INDIA
| | - Phu K. Tang
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
- Present Address: Flatiron Institute, New York, NY, 10010, United States
- These authors contributed equally: Phu K. Tang, Abhik Ghosh Moulick, and Rutika Patel
| | - Abhik Ghosh Moulick
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- These authors contributed equally: Phu K. Tang, Abhik Ghosh Moulick, and Rutika Patel
| | - Rutika Patel
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
- These authors contributed equally: Phu K. Tang, Abhik Ghosh Moulick, and Rutika Patel
| | - Anjela Manandhar
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
- Present Address: Takeda Pharmaceuticals, Boston, MA, 02139, United States
| | - Sharon M. Loverde
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New York, 10314, United States
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, United States
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY, 10016, United States
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14
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Meng L, Wu B, OuYang L, Peng R, Chen Y, Tang Z, Zhang M, Xu T, Wang Y, Lu S, Jing X, Fu S. Electroacupuncture regulates histone acetylation of Bcl-2 and Caspase-3 genes to improve ischemic stroke injury. Heliyon 2024; 10:e27045. [PMID: 38500994 PMCID: PMC10945129 DOI: 10.1016/j.heliyon.2024.e27045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 12/16/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
Background Imbalances between Bcl-2 and caspase-3 are significant evidence of apoptosis, which is considered an influential factor in rapidly occurring neuronal cell death and the decline of neurological function after stroke. Studies have shown that acupuncture can reduce poststroke brain cell damage via either an increase in Bcl-2 or a reduction in caspase-3 exposure. The current study aimed to investigate whether acupuncture could modulate Bcl-2 and caspase-3 expression through histone acetylation modifications, which could potentially serve as a neuroprotective mechanism. Methods This study used TTC staining, Nissl staining, Clark neurological system score, and Evans Blue (EB) extravasation to evaluate neurological damage following stroke. The expression of Bcl-2/caspase-3 mRNA was detected by real-time fluorescence quantification of PCR (real-time PCR), whereas the protein expression levels of Bcl-2, Bax, caspase-3, and cleaved caspase-3 were assessed using western blotting. TUNEL staining of the ischemic cortical neurons determined apoptosis in the ischemic cortex. Histone acetyltransferase (HAT) and histone deacetylase (HDAC) activities, along with the protein performance of AceH3, H3K9ace, and H3K27ace, were detected to evaluate the degree of histone acetylation. The acetylation enrichment levels of H3K9 and K3K27 in the Bcl-2/caspase-3 gene were assessed using Chromatin Immunoprecipitation (ChIP) assay. Results Our data demonstrated that electroacupuncture (EA) exerts a significant neuroprotective effect in middle cerebral artery occlusion (MCAO) rats, as evidenced by a reduction in infarct volume, neuronal damage, Blood-Brain Barrier (BBB) disruption, and decreased apoptosis of ischemic cortical neurons. EA treatment can promote the mRNA and protein expression of the Bcl-2 gene in the ischemic brain while reducing the mRNA and protein expression levels of caspase-3 and effectively decreasing the protein expression levels of Bax and cleaved caspase-3. More importantly, EA treatment enhanced the level of histone acetylation, including Ace-H3, H3K9ace, and H3K27ace, significantly enhanced the occupancy of H3K9ace/H3K27ace at the Bcl-2 promoter, and reduced the enrichment of H3K9ace and H3K27ace at the caspase-3 promoter. However, the Histone Acetyltransferase inhibitor (HATi) treatment reversed these effects. Conclusions Our data demonstrated that EA mediated the expression levels of Bcl-2 and caspase-3 in MCAO rats by regulating the occupancy of acetylated H3K9/H3K27 at the promoters of these two genes, thus exerting a cerebral protective effect in ischemic reperfusion (I/R) injury.
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Affiliation(s)
| | | | - Ling OuYang
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Rou Peng
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yonglin Chen
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhijuan Tang
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Min Zhang
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Tanqing Xu
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yaling Wang
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shengfeng Lu
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xinyue Jing
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shuping Fu
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210023, China
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15
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Huang R, Irish VF. An epigenetic timer regulates the transition from cell division to cell expansion during Arabidopsis petal organogenesis. PLoS Genet 2024; 20:e1011203. [PMID: 38442104 PMCID: PMC10942257 DOI: 10.1371/journal.pgen.1011203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 03/15/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
A number of studies have demonstrated that epigenetic factors regulate plant developmental timing in response to environmental changes. However, we still have an incomplete view of how epigenetic factors can regulate developmental events such as organogenesis, and the transition from cell division to cell expansion, in plants. The small number of cell types and the relatively simple developmental progression required to form the Arabidopsis petal makes it a good model to investigate the molecular mechanisms driving plant organogenesis. In this study, we investigated how the RABBIT EARS (RBE) transcriptional repressor maintains the downregulation of its downstream direct target, TCP5, long after RBE expression dissipates. We showed that RBE recruits the Groucho/Tup1-like corepressor TOPLESS (TPL) to repress TCP5 transcription in petal primordia. This process involves multiple layers of changes such as remodeling of chromatin accessibility, alteration of RNA polymerase activity, and histone modifications, resulting in an epigenetic memory that is maintained through multiple cell divisions. This memory functions to maintain cell divisions during the early phase of petal development, and its attenuation in a cell division-dependent fashion later in development enables the transition from cell division to cell expansion. Overall, this study unveils a novel mechanism by which the memory of an epigenetic state, and its cell-cycle regulated decay, acts as a timer to precisely control organogenesis.
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Affiliation(s)
- Ruirui Huang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Vivian F. Irish
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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Betti MJ, Aldrich MC, Gamazon ER. Minimum entropy framework identifies a novel class of genomic functional elements and reveals regulatory mechanisms at human disease loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.544507. [PMID: 37398170 PMCID: PMC10312628 DOI: 10.1101/2023.06.11.544507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We introduce CoRE-BED, a framework trained using 19 epigenomic features in 33 major cell and tissue types to predict cell-type-specific regulatory function. CoRE-BED identifies nine functional classes de-novo, capturing both known and new regulatory categories. Notably, we describe a previously undercharacterized class that we term Development Associated Elements (DAEs), which are highly enriched in cell types with elevated regenerative potential and distinguished by the dual presence of either H3K4me2 and H3K9ac (an epigenetic signature associated with kinetochore assembly) or H3K79me3 and H4K20me1 (a signature associated with transcriptional pause release). Unlike bivalent promoters, which represent a transitory state between active and silenced promoters, DAEs transition directly to or from a non-functional state during stem cell differentiation and are proximal to highly expressed genes. CoRE-BED's interpretability facilitates causal inference and functional prioritization. Across 70 complex traits, distal insulators account for the largest mean proportion of SNP heritability (~49%) captured by the GWAS. Collectively, our results demonstrate the value of exploring non-conventional ways of regulatory classification that enrich for trait heritability, to complement existing approaches for cis-regulatory prediction.
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Affiliation(s)
| | | | - Eric R Gamazon
- Vanderbilt University Medical Center, Nashville, TN
- Clare Hall, University of Cambridge, Cambridge, England
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17
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Khan P, Singha P, Nag Chaudhuri R. RNA Polymerase II Dependent Crosstalk between H4K16 Deacetylation and H3K56 Acetylation Promotes Transcription of Constitutively Expressed Genes. Mol Cell Biol 2023; 43:596-610. [PMID: 37937370 PMCID: PMC10761024 DOI: 10.1080/10985549.2023.2270912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
Nucleosome dynamics in the coding region of a transcriptionally active locus is critical for understanding how RNA polymerase II progresses through the gene body. Histone acetylation and deacetylation critically influence nucleosome accessibility during DNA metabolic processes like transcription. Effect of such histone modifications is context and residue dependent. Rather than effect of individual histone residues, the network of modifications of several histone residues in combination generates a chromatin landscape that is conducive for transcription. Here we show that in Saccharomyces cerevisiae, crosstalk between deacetylation of the H4 N-terminal tail residue H4K16 and acetylation of the H3 core domain residue H3K56, promotes RNA polymerase II progression through the gene body. Results indicate that deacetylation of H4K16 precedes and in turn induces H3K56 acetylation. Effectively, recruitment of Rtt109, the HAT responsible for H3K56 acetylation is essentially dependent on H4K16 deacetylation. In Hos2 deletion strains, where H4K16 deacetylation is abolished, both H3K56 acetylation and RNA polymerase II recruitment gets significantly impaired. Notably, H4K16 deacetylation and H3K56 acetylation are found to be essentially dependent on active transcription. In summary, H4K16 deacetylation promotes H3K56 acetylation and the two modifications together work towards successful functioning of RNA polymerase II during active transcription.
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Affiliation(s)
- Preeti Khan
- Department of Biotechnology, St Xavier’s College, Kolkata, India
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18
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Wille CK, Zhang X, Haws SA, Denu JM, Sridharan R. DOT1L is a barrier to histone acetylation during reprogramming to pluripotency. SCIENCE ADVANCES 2023; 9:eadf3980. [PMID: 37976354 PMCID: PMC10656071 DOI: 10.1126/sciadv.adf3980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Embryonic stem cells (ESCs) have transcriptionally permissive chromatin enriched for gene activation-associated histone modifications. A striking exception is DOT1L-mediated H3K79 dimethylation (H3K79me2) that is considered a positive regulator of transcription. We find that ESCs are depleted for H3K79me2 at shared locations of enrichment with somatic cells, which are highly and ubiquitously expressed housekeeping genes, and have lower RNA polymerase II (RNAPII) at the transcription start site (TSS) despite greater nascent transcription. Inhibiting DOT1L increases the efficiency of reprogramming of somatic to induced pluripotent stem cells, enables an ESC-like RNAPII pattern at the TSS, and functionally compensates for enforced RNAPII pausing. DOT1L inhibition increases H3K27 methylation and RNAPII elongation-enhancing histone acetylation without changing the expression of the causal histone-modifying enzymes. Only the maintenance of elevated histone acetylation is essential for enhanced reprogramming and occurs at loci that are depleted for H3K79me2. Thus, DOT1L inhibition promotes the hyperacetylation and hypertranscription pluripotent properties.
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Affiliation(s)
- Coral K. Wille
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Xiaoya Zhang
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer A. Haws
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John M. Denu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, 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 53705, USA
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Żabka A, Gocek N, Polit JT, Maszewski J. Epigenetic modifications evidenced by isolation of proteins on nascent DNA and immunofluorescence in hydroxyurea-treated root meristem cells of Vicia faba. PLANTA 2023; 258:95. [PMID: 37814174 PMCID: PMC10562345 DOI: 10.1007/s00425-023-04249-2] [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: 05/15/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023]
Abstract
MAIN CONCLUSION By implementation of the iPOND technique for plant material, changes in posttranslational modifications of histones were identified in hydroxyurea-treated root meristem cells of Vicia. Replication stress (RS) disrupts or inhibits replication forks and by altering epigenetic information of the newly formed chromatin can affect gene regulation and/or spatial organisation of DNA. Experiments on Vicia faba root meristem cells exposed to short-term treatment with 3 mM hydroxyurea (HU, an inhibitor of DNA replication) were aimed to understand epigenetic changes related to RS. To achieve this, the following histone modifications were studied using isolation of proteins on nascent DNA (iPOND) technique (for the first time on plant material) combined with immunofluorescence labeling: (i) acetylation of histone H3 at lysine 56 (H3K56Ac), (ii) acetylation of histone H4 at Lys 5 (H4K5Ac), and (iii) phosphorylation of histone H3 at threonine 45 (H3T45Ph). Certainly, the implementation of the iPOND method for plants may prove to be a key step for a more in-depth understanding of the cell's response to RS at the chromatin level.
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Affiliation(s)
- Aneta Żabka
- Faculty of Biology and Environmental Protection Department of Cytophysiology, University of Lodz, 90-236, Lodz, Poland.
| | - Natalia Gocek
- Faculty of Biology and Environmental Protection Department of Cytophysiology, University of Lodz, 90-236, Lodz, Poland
| | - Justyna Teresa Polit
- Faculty of Biology and Environmental Protection Department of Cytophysiology, University of Lodz, 90-236, Lodz, Poland
| | - Janusz Maszewski
- Faculty of Biology and Environmental Protection Department of Cytophysiology, University of Lodz, 90-236, Lodz, Poland
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Zhong B, Liao Q, Wang X, Wang X, Zhang J. The roles of epigenetic regulation in cholangiocarcinogenesis. Biomed Pharmacother 2023; 166:115290. [PMID: 37557012 DOI: 10.1016/j.biopha.2023.115290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023] Open
Abstract
Cholangiocarcinoma (CCA), a heterogeneous malignancy of bile duct epithelial cells, is characterized by aggressiveness, difficult diagnosis, and poor prognosis due to limited understanding and lack of effective therapeutic strategies. Genetic and epigenetic alterations accumulated in CCA cells can cause the aberrant regulation of oncogenes and tumor suppressors. Epigenetic alterations with histone modification, DNA methylation, and noncoding RNA modulation are associated with the carcinogenesis of CCA. Mutation or silencing of genes by various mechanisms can be a frequent event during CCA development. Alterations in histone acetylation/deacetylation at the posttranslational level, DNA methylation at promoters, and noncoding RNA regulation contribute to the heterogeneity of CCA and drive tumor development. In this review article, we mainly focus on the roles of epigenetic regulation in cholangiocarcinogenesis. Alterations in epigenetic modification can be potential targets for the therapeutic management of CCA, and epigenetic targets may become diagnostic biomarkers of CCA.
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Affiliation(s)
- Baiyin Zhong
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Qicheng Liao
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Xin Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Xiaonong Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Jianhong Zhang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China; Ganzhou Key Laboratory of Hepatocellular Carcinoma, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China.
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21
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Lin H, Song Y, Song L, Geng Z, Cheng R, Lei Y, Guo F. Inhibition of Heat Shock-Induced H3K9ac Reduction Sensitizes Cancer Cells to Hyperthermia. Int J Biol Sci 2023; 19:4849-4864. [PMID: 37781518 PMCID: PMC10539700 DOI: 10.7150/ijbs.86384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/11/2023] [Indexed: 10/03/2023] Open
Abstract
Heat stress, clinically known as hyperthermia, is a promising adjunctive modality in cancer treatment. However, the efficacy of hyperthermia as a monotherapy is limited and the underlying mechanism remains poorly understood. Targeting histone modifications is an emerging strategy for cancer therapy, but little is known regarding the role of heat stress in altering these modifications. Here, we report that heat shock inhibits H3K9 acetylation (H3K9ac) via histone deacetylase 6 (HDAC6) regulation. Heat shock inhibits the interaction between HDAC6 and heat shock protein 90 (HSP90), enhances nuclear localization of HDAC6, and promotes HDAC6 phosphorylation, which is regulated by protein phosphatase 2A (PP2A). Combining hyperthermia with HDAC inhibitors vorinostat or panobinostat leads to better anti-cancer effects compared to monotherapy. KEAP1 and DPP7 as genes affected by heat-induced inhibition of H3K9ac, and combining them with hyperthermia can better induce apoptosis in tumor cells. This study reveals previously unknown mechanisms of H3K9ac decreased by heat shock in cancer cells and highlights a potential combinational therapy involving hyperthermia and targeting of these new mechanisms.
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Affiliation(s)
- Huiyun Lin
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dong chuan Road, Shanghai 200240, China
| | - Yihui Song
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dong chuan Road, Shanghai 200240, China
| | - Lingjun Song
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Hai-Ning Road, Shanghai 200080, China
| | - Zilong Geng
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dong chuan Road, Shanghai 200240, China
| | - Runtan Cheng
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dong chuan Road, Shanghai 200240, China
| | - Yinrui Lei
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dong chuan Road, Shanghai 200240, China
| | - Fang Guo
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dong chuan Road, Shanghai 200240, China
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22
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Iuso D, Garcia-Saez I, Couté Y, Yamaryo-Botté Y, Boeri Erba E, Adrait A, Zeaiter N, Tokarska-Schlattner M, Jilkova ZM, Boussouar F, Barral S, Signor L, Couturier K, Hajmirza A, Chuffart F, Bourova-Flin E, Vitte AL, Bargier L, Puthier D, Decaens T, Rousseaux S, Botté C, Schlattner U, Petosa C, Khochbin S. Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet. SCIENCE ADVANCES 2023; 9:eadh0140. [PMID: 37672589 PMCID: PMC10482350 DOI: 10.1126/sciadv.adh0140] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 08/02/2023] [Indexed: 09/08/2023]
Abstract
The synthesis of fatty acids from acetyl-coenzyme A (AcCoA) is deregulated in diverse pathologies, including cancer. Here, we report that fatty acid accumulation is negatively regulated by nucleoside diphosphate kinases 1 and 2 (NME1/2), housekeeping enzymes involved in nucleotide homeostasis that were recently found to bind CoA. We show that NME1 additionally binds AcCoA and that ligand recognition involves a unique binding mode dependent on the CoA/AcCoA 3' phosphate. We report that Nme2 knockout mice fed a high-fat diet (HFD) exhibit excessive triglyceride synthesis and liver steatosis. In liver cells, NME2 mediates a gene transcriptional response to HFD leading to the repression of fatty acid accumulation and activation of a protective gene expression program via targeted histone acetylation. Our findings implicate NME1/2 in the epigenetic regulation of a protective liver response to HFD and suggest a potential role in controlling AcCoA usage between the competing paths of histone acetylation and fatty acid synthesis.
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Affiliation(s)
- Domenico Iuso
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Isabel Garcia-Saez
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble 38000, France
| | - Yoshiki Yamaryo-Botté
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Annie Adrait
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble 38000, France
| | - Nour Zeaiter
- Univ. Grenoble Alpes, INSERM, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | | | - Zuzana Macek Jilkova
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
- CHU Grenoble Alpes, Service d’hépato-gastroentérologie, Pôle Digidune, La Tronche 38700, France
| | - Fayçal Boussouar
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Sophie Barral
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Karine Couturier
- Univ. Grenoble Alpes, INSERM, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | - Azadeh Hajmirza
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Florent Chuffart
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Ekaterina Bourova-Flin
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Anne-Laure Vitte
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Lisa Bargier
- Aix Marseille Université, INSERM, TAGC, TGML, Marseille 13288, France
| | - Denis Puthier
- Aix Marseille Université, INSERM, TAGC, TGML, Marseille 13288, France
| | - Thomas Decaens
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
- CHU Grenoble Alpes, Service d’hépato-gastroentérologie, Pôle Digidune, La Tronche 38700, France
| | - Sophie Rousseaux
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Cyrille Botté
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
| | - Uwe Schlattner
- Univ. Grenoble Alpes, INSERM, Institut Universitaire de France, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | - Carlo Petosa
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
| | - Saadi Khochbin
- Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France
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23
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Li J, Cao Y, Yang Y, Ma H, Zhao J, Zhang Y, Liu N. Quantitative Acetylomics Reveals Substrates of Lysine Acetyltransferase GCN5 in Adult and Aging Drosophila. J Proteome Res 2023; 22:2909-2924. [PMID: 37545086 DOI: 10.1021/acs.jproteome.3c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Protein lysine acetylation is a dynamic post-translational modification (PTM) that regulates a wide spectrum of cellular events including aging. General control nonderepressible 5 (GCN5) is a highly conserved lysine acetyltransferase (KAT). However, the acetylation substrates of GCN5 in vivo remain poorly studied, and moreover, how lysine acetylation changes with age and the contribution of KATs to aging remain to be addressed. Here, using Drosophila, we perform label-free quantitative acetylomic analysis, identifying new substrates of GCN5 in the adult and aging process. We further characterize the dynamics of protein acetylation with age, which exhibits a trend of increase. Since the expression of endogenous fly Gcn5 progressively increases during aging, we reason that, by combining the substrate analysis, the increase in acetylation with age is triggered, at least in part, by GCN5. Collectively, our study substantially expands the atlas of GCN5 substrates in vivo, provides a resource of protein acetylation that naturally occurs with age, and demonstrates how individual KAT contributes to the aging acetylome.
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Affiliation(s)
- Jingshu Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ye Cao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanhuan Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Zhao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- Shanghai Key Laboratory of Aging Studies, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
| | - Nan Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
- Shanghai Key Laboratory of Aging Studies, 100 Hai Ke Rd., Pudong, Shanghai 201210, China
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24
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Qiu X, Liang G, Zhou W, Sen R, Atchison ML. Multiple lineage-specific epigenetic landscapes at the antigen receptor loci. AGING RESEARCH (HONG KONG, CHINA) 2023; 1:9340010. [PMID: 38770228 PMCID: PMC11103674 DOI: 10.26599/agr.2023.9340010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Antigen receptors (AgRs) expressed on B and T cells provide the adaptive immune system with ability to detect numerous foreign antigens. Epigenetic features of B cell receptor (BCR) and T cell receptor (TCR) genes were previously studied in lymphocytes, but little is known about their epigenetic features in other cells. Here, we explored histone modifications and transcription markers at the BCR and TCR loci in lymphocytes (pro-B, DP T cells, and mature CD4+ T cells), compared to embryonic stem (ES) cells and neurons. In B cells, the BCR loci exhibited active histone modifications and transcriptional markers indicative of active loci. Similar results were observed at the TCR loci in T cells. All loci were largely inactive in neurons. Surprisingly, in ES cells all AgR loci displayed a high degree of active histone modifications and markers of active transcription. Locations of these active histone modifications in ES cells were largely distinct from those in pro-B cells, and co-localized at numerous binding locations for transcription factors Oct4, Sox2, and Nanog. ES and pro-B cells also showed distinct binding patterns for the ubiquitous transcription factor YY1 and chromatin remodeler Brg1. On the contrary, there were many overlapping CCCTC-binding factor (CTCF) binding patterns when comparing ES cells, pro-B cells, and neurons. Our study identifies epigenetic features in ES cells and lymphocytes that may be related to ES cell pluripotency and lymphocyte tissue-specific activation at the AgR loci.
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Affiliation(s)
- Xiang Qiu
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland 21224, USA
| | - Guanxiang Liang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland 21224, USA
| | - Michael L. Atchison
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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25
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Otlu B, Díaz-Gay M, Vermes I, Bergstrom EN, Zhivagui M, Barnes M, Alexandrov LB. Topography of mutational signatures in human cancer. Cell Rep 2023; 42:112930. [PMID: 37540596 PMCID: PMC10507738 DOI: 10.1016/j.celrep.2023.112930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 05/09/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023] Open
Abstract
The somatic mutations found in a cancer genome are imprinted by different mutational processes. Each process exhibits a characteristic mutational signature, which can be affected by the genome architecture. However, the interplay between mutational signatures and topographical genomic features has not been extensively explored. Here, we integrate mutations from 5,120 whole-genome-sequenced tumors from 40 cancer types with 516 topographical features from ENCODE to evaluate the effect of nucleosome occupancy, histone modifications, CTCF binding, replication timing, and transcription/replication strand asymmetries on the cancer-specific accumulation of mutations from distinct mutagenic processes. Most mutational signatures are affected by topographical features, with signatures of related etiologies being similarly affected. Certain signatures exhibit periodic behaviors or cancer-type-specific enrichments/depletions near topographical features, revealing further information about the processes that imprinted them. Our findings, disseminated via the COSMIC (Catalog of Somatic Mutations in Cancer) signatures database, provide a comprehensive online resource for exploring the interactions between mutational signatures and topographical features across human cancer.
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Affiliation(s)
- Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA; Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara 06800, Turkey
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ian Vermes
- COSMIC, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Erik N Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Maria Zhivagui
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA.
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26
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Lee RS, Sad K, Fawwal DV, Spangle JM. Emerging Role of Epigenetic Modifiers in Breast Cancer Pathogenesis and Therapeutic Response. Cancers (Basel) 2023; 15:4005. [PMID: 37568822 PMCID: PMC10417282 DOI: 10.3390/cancers15154005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/13/2023] Open
Abstract
Breast cancer pathogenesis, treatment, and patient outcomes are shaped by tumor-intrinsic genomic alterations that divide breast tumors into molecular subtypes. These molecular subtypes often dictate viable therapeutic interventions and, ultimately, patient outcomes. However, heterogeneity in therapeutic response may be a result of underlying epigenetic features that may further stratify breast cancer patient outcomes. In this review, we examine non-genetic mechanisms that drive functional changes to chromatin in breast cancer to contribute to cell and tumor fitness and highlight how epigenetic activity may inform the therapeutic response. We conclude by providing perspectives on the future of therapeutic targeting of epigenetic enzymes, an approach that holds untapped potential to improve breast cancer patient outcomes.
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Affiliation(s)
- Richard Sean Lee
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
- Department of Biology, Emory College, Atlanta, GA 30322, USA
| | - Kirti Sad
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
| | - Dorelle V. Fawwal
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University School of Medicine, Atlanta, GA 30311, USA
| | - Jennifer Marie Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
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27
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Zhang X, Noberini R, Vai A, Bonaldi T, Seidl MF, Collemare J. Detection and quantification of the histone code in the fungal genus Aspergillus. Fungal Genet Biol 2023; 167:103800. [PMID: 37146898 DOI: 10.1016/j.fgb.2023.103800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/30/2023] [Accepted: 04/24/2023] [Indexed: 05/07/2023]
Abstract
In eukaryotes, the combination of different histone post-translational modifications (PTMs) - the histone code - impacts the chromatin organization as compact and transcriptionally silent heterochromatin or accessible and transcriptionally active euchromatin. Although specific histone PTMs have been studied in fungi, an overview of histone PTMs and their relative abundance is still lacking. Here, we used mass spectrometry to detect and quantify histone PTMs in three fungal species belonging to three distinct taxonomic sections of the genus Aspergillus (Aspergillus niger, Aspergillus nidulans (two strains), and Aspergillus fumigatus). We overall detected 23 different histone PTMs, including a majority of lysine methylations and acetylations, and 23 co-occurrence patterns of multiple histone PTMs. Among those, we report for the first time the detection of H3K79me1, H3K79me2, and H4K31ac in Aspergilli. Although all three species harbour the same PTMs, we found significant differences in the relative abundance of H3K9me1/2/3, H3K14ac, H3K36me1 and H3K79me1, as well as the co-occurrence of acetylation on both K18 and K23 of histone H3 in a strain-specific manner. Our results provide novel insights about the underexplored complexity of the histone code in filamentous fungi, and its functional implications on genome architecture and gene regulation.
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Affiliation(s)
- Xin Zhang
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Alessandro Vai
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Oncology and Haematology-Oncology, University of Milano, Via Santa Sofia 9/1, 20122 Milano, Italy.
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Jérȏme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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28
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Jiang D, Li T, Guo C, Tang TS, Liu H. Small molecule modulators of chromatin remodeling: from neurodevelopment to neurodegeneration. Cell Biosci 2023; 13:10. [PMID: 36647159 PMCID: PMC9841685 DOI: 10.1186/s13578-023-00953-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
The dynamic changes in chromatin conformation alter the organization and structure of the genome and further regulate gene transcription. Basically, the chromatin structure is controlled by reversible, enzyme-catalyzed covalent modifications to chromatin components and by noncovalent ATP-dependent modifications via chromatin remodeling complexes, including switch/sucrose nonfermentable (SWI/SNF), inositol-requiring 80 (INO80), imitation switch (ISWI) and chromodomain-helicase DNA-binding protein (CHD) complexes. Recent studies have shown that chromatin remodeling is essential in different stages of postnatal and adult neurogenesis. Chromatin deregulation, which leads to defects in epigenetic gene regulation and further pathological gene expression programs, often causes a wide range of pathologies. This review first gives an overview of the regulatory mechanisms of chromatin remodeling. We then focus mainly on discussing the physiological functions of chromatin remodeling, particularly histone and DNA modifications and the four classes of ATP-dependent chromatin-remodeling enzymes, in the central and peripheral nervous systems under healthy and pathological conditions, that is, in neurodegenerative disorders. Finally, we provide an update on the development of potent and selective small molecule modulators targeting various chromatin-modifying proteins commonly associated with neurodegenerative diseases and their potential clinical applications.
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Affiliation(s)
- Dongfang Jiang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingting Li
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Caixia Guo
- grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tie-Shan Tang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongmei Liu
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
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29
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Princová J, Salat-Canela C, Daněk P, Marešová A, de Cubas L, Bähler J, Ayté J, Hidalgo E, Převorovský M. Perturbed fatty-acid metabolism is linked to localized chromatin hyperacetylation, increased stress-response gene expression and resistance to oxidative stress. PLoS Genet 2023; 19:e1010582. [PMID: 36626368 PMCID: PMC9870116 DOI: 10.1371/journal.pgen.1010582] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/23/2023] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Oxidative stress is associated with cardiovascular and neurodegenerative diseases, diabetes, cancer, psychiatric disorders and aging. In order to counteract, eliminate and/or adapt to the sources of stress, cells possess elaborate stress-response mechanisms, which also operate at the level of regulating transcription. Interestingly, it is becoming apparent that the metabolic state of the cell and certain metabolites can directly control the epigenetic information and gene expression. In the fission yeast Schizosaccharomyces pombe, the conserved Sty1 stress-activated protein kinase cascade is the main pathway responding to most types of stresses, and regulates the transcription of hundreds of genes via the Atf1 transcription factor. Here we report that fission yeast cells defective in fatty acid synthesis (cbf11, mga2 and ACC/cut6 mutants; FAS inhibition) show increased expression of a subset of stress-response genes. This altered gene expression depends on Sty1-Atf1, the Pap1 transcription factor, and the Gcn5 and Mst1 histone acetyltransferases, is associated with increased acetylation of histone H3 at lysine 9 in the corresponding gene promoters, and results in increased cellular resistance to oxidative stress. We propose that changes in lipid metabolism can regulate the chromatin and transcription of specific stress-response genes, which in turn might help cells to maintain redox homeostasis.
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Affiliation(s)
- Jarmila Princová
- Laboratory of Microbial Genomics, Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Clàudia Salat-Canela
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader, Barcelona, Spain
| | - Petr Daněk
- Laboratory of Microbial Genomics, Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Anna Marešová
- Laboratory of Microbial Genomics, Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Laura de Cubas
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader, Barcelona, Spain
| | - Jürg Bähler
- Institute of Healthy Ageing and Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader, Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Dr. Aiguader, Barcelona, Spain
| | - Martin Převorovský
- Laboratory of Microbial Genomics, Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail:
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Harati J, Liu K, Shahsavarani H, Du P, Galluzzi M, Deng K, Mei J, Chen HY, Bonakdar S, Aflatoonian B, Hou G, Zhu Y, Pan H, Wong RCB, Shokrgozar MA, Song W, Wang PY. Defined Physicochemical Cues Steering Direct Neuronal Reprogramming on Colloidal Self-Assembled Patterns (cSAPs). ACS NANO 2022; 17:1054-1067. [PMID: 36583476 DOI: 10.1021/acsnano.2c07473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Direct neuronal reprogramming of somatic cells into induced neurons (iNs) has been recently established as a promising approach to generating neuron cells. Previous studies have reported that the biophysical cues of the in vitro microenvironment are potent modulators in the cell fate decision; thus, the present study explores the effects of a customized pattern (named colloidal self-assembled patterns, cSAPs) on iN generation from human fibroblasts using small molecules. The result revealed that the cSAP, composed of binary particles in a hexagonal-close-packed (hcp) geometry, is capable of improving neuronal reprogramming efficiency and steering the ratio of the iN subtypes. Cells exhibited distinct cell morphology, upregulated cell adhesion markers (i.e., SDC1 and ITGAV), enriched signaling pathways (i.e., Hippo and Wnt), and chromatin remodeling on the cSAP compared to those on the control substrates. The result also showed that the iN subtype specification on cSAP was surface-dependent; therefore, the defined physicochemical cue from each cSAP is exclusive. Our findings show that direct cell reprogramming can be manipulated through specific biophysical cues on the artificial matrix, which is significant in cell transdifferentiation and lineage conversion.
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Affiliation(s)
- Javad Harati
- Lab Regenerative Medicine and Biomedical Innovations, Pasteur Institute of Iran, Tehran1316943551, Iran
- Oujiang Laboratory, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang325000, People's Republic of China
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong518055, People's Republic of China
- University of Chinese Academy of Science, Beijing101408, People's Republic of China
| | - Kun Liu
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong518055, People's Republic of China
| | - Hosein Shahsavarani
- Lab Regenerative Medicine and Biomedical Innovations, Pasteur Institute of Iran, Tehran1316943551, Iran
- Oujiang Laboratory, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang325000, People's Republic of China
- Department of Cell and Molecular Biology, Faculty of Life Science and Biotechnology, Shahid Beheshti University, Tehran1983969411, Iran
| | - Ping Du
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong518055, People's Republic of China
| | - Massimiliano Galluzzi
- Materials Interfaces Center, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong518055, People's Republic of China
| | - Ke Deng
- School of Food and Bioengineering, Xihua University, Chengdu610097, People's Republic of China
| | - Jei Mei
- Oujiang Laboratory, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang325000, People's Republic of China
| | - Hsien-Yeh Chen
- Department of Chemical Engineering, National Taiwan University, Taipei10617, Taiwan
| | - Shahin Bonakdar
- Lab Regenerative Medicine and Biomedical Innovations, Pasteur Institute of Iran, Tehran1316943551, Iran
| | - Behrouz Aflatoonian
- Stem Cell Biology Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd8916188635, Iran
| | - Guoqiang Hou
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong518055, People's Republic of China
| | - Yingjie Zhu
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong518055, People's Republic of China
| | - Haobo Pan
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong518055, People's Republic of China
| | - Raymond C B Wong
- Centre for Eye Research Australia, Department of Surgery, University of Melbourne, Parkville, Victoria3002, Australia
| | - Mohammad Ali Shokrgozar
- Lab Regenerative Medicine and Biomedical Innovations, Pasteur Institute of Iran, Tehran1316943551, Iran
| | - Weihong Song
- Oujiang Laboratory, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang325000, People's Republic of China
| | - Peng-Yuan Wang
- Oujiang Laboratory, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang325000, People's Republic of China
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong518055, People's Republic of China
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Niewiadomska-Cimicka A, Hache A, Le Gras S, Keime C, Ye T, Eisenmann A, Harichane I, Roux MJ, Messaddeq N, Clérin E, Léveillard T, Trottier Y. Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy. J Biomed Sci 2022; 29:107. [PMID: 36539812 PMCID: PMC9768914 DOI: 10.1186/s12929-022-00892-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disorder that primarily affects the cerebellum and retina. SCA7 is caused by a polyglutamine expansion in the ATXN7 protein, a subunit of the transcriptional coactivator SAGA that acetylates histone H3 to deposit narrow H3K9ac mark at DNA regulatory elements of active genes. Defective histone acetylation has been presented as a possible cause for gene deregulation in SCA7 mouse models. However, the topography of acetylation defects at the whole genome level and its relationship to changes in gene expression remain to be determined. METHODS We performed deep RNA-sequencing and chromatin immunoprecipitation coupled to high-throughput sequencing to examine the genome-wide correlation between gene deregulation and alteration of the active transcription marks, e.g. SAGA-related H3K9ac, CBP-related H3K27ac and RNA polymerase II (RNAPII), in a SCA7 mouse retinopathy model. RESULTS Our analyses revealed that active transcription marks are reduced at most gene promoters in SCA7 retina, while a limited number of genes show changes in expression. We found that SCA7 retinopathy is caused by preferential downregulation of hundreds of highly expressed genes that define morphological and physiological identities of mature photoreceptors. We further uncovered that these photoreceptor genes harbor unusually broad H3K9ac profiles spanning the entire gene bodies and have a low RNAPII pausing. This broad H3K9ac signature co-occurs with other features that delineate superenhancers, including broad H3K27ac, binding sites for photoreceptor specific transcription factors and expression of enhancer-related non-coding RNAs (eRNAs). In SCA7 retina, downregulated photoreceptor genes show decreased H3K9 and H3K27 acetylation and eRNA expression as well as increased RNAPII pausing, suggesting that superenhancer-related features are altered. CONCLUSIONS Our study thus provides evidence that distinctive epigenetic configurations underlying high expression of cell-type specific genes are preferentially impaired in SCA7, resulting in a defect in the maintenance of identity features of mature photoreceptors. Our results also suggest that continuous SAGA-driven acetylation plays a role in preserving post-mitotic neuronal identity.
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Affiliation(s)
- Anna Niewiadomska-Cimicka
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Antoine Hache
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Stéphanie Le Gras
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Céline Keime
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Tao Ye
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Aurelie Eisenmann
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Imen Harichane
- grid.462844.80000 0001 2308 1657Department of Genetics, INSERM, CNRS, Institut de la Vision, Sorbonne University, 75012 Paris, France
| | - Michel J. Roux
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Nadia Messaddeq
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
| | - Emmanuelle Clérin
- grid.462844.80000 0001 2308 1657Department of Genetics, INSERM, CNRS, Institut de la Vision, Sorbonne University, 75012 Paris, France
| | - Thierry Léveillard
- grid.462844.80000 0001 2308 1657Department of Genetics, INSERM, CNRS, Institut de la Vision, Sorbonne University, 75012 Paris, France
| | - Yvon Trottier
- grid.11843.3f0000 0001 2157 9291Institute of Genetics and Molecular and Cellular Biology (IGBMC), INSERM U1258, CNRS UMR7104, University of Strasbourg, 67404 Illkirch, France
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Fukuda Y, Akematsu T, Bando H, Kato K. Snf2 Proteins Are Required to Generate Gamete Pronuclei in Tetrahymena thermophila. Microorganisms 2022; 10:microorganisms10122426. [PMID: 36557679 PMCID: PMC9786623 DOI: 10.3390/microorganisms10122426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
During sexual reproduction/conjugation of the ciliate Tetrahymena thermophila, the germinal micronucleus undergoes meiosis resulting in four haploid micronuclei (hMICs). All hMICs undergo post-meiotic DNA double-strand break (PM-DSB) formation, cleaving their genome. DNA lesions are subsequently repaired in only one ‘selected’ hMIC, which eventually produces gametic pronuclei. DNA repair in the selected hMIC involves chromatin remodeling by switching from the heterochromatic to the euchromatic state of its genome. Here, we demonstrate that, among the 15 Tetrahymena Snf2 family proteins, a core of the ATP-dependent chromatin remodeling complex in Tetrahymena, the germline nucleus specific Iswi in Tetrahymena IswiGTt and Rad5Tt is crucial for the generation of gametic pronuclei. In either gene knockout, the selected hMIC which shows euchromatin markers such as lysine-acetylated histone H3 does not appear, but all hMICs in which markers for DNA lesions persist are degraded, indicating that both IswiGTt and Rad5Tt have important roles in repairing PM-DSB DNA lesions and remodeling chromatin for the euchromatic state in the selected hMIC.
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Affiliation(s)
- Yasuhiro Fukuda
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
- Correspondence: ; Tel.: +81-229-84-7387
| | - Takahiko Akematsu
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo 156-8550, Japan
| | - Hironori Bando
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
| | - Kentaro Kato
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
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33
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Hu X, Jin X, Cao X, Liu B. The Anaphase-Promoting Complex/Cyclosome Is a Cellular Ageing Regulator. Int J Mol Sci 2022; 23:ijms232315327. [PMID: 36499653 PMCID: PMC9740938 DOI: 10.3390/ijms232315327] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/11/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a complicated cellular component that plays significant roles in regulating the cell cycle process of eukaryotic organisms. The spatiotemporal regulation mechanisms of APC/C in distinct cell cycle transitions are no longer mysterious, and the components of this protein complex are gradually identified and characterized. Given the close relationship between the cell cycle and lifespan, it is urgent to understand the roles of APC/C in lifespan regulation, but this field still seems to have not been systematically summarized. Furthermore, although several reviews have reported the roles of APC/C in cancer, there are still gaps in the summary of its roles in other age-related diseases. In this review, we propose that the APC/C is a novel cellular ageing regulator based on its indispensable role in the regulation of lifespan and its involvement in age-associated diseases. This work provides an extensive review of aspects related to the underlying mechanisms of APC/C in lifespan regulation and how it participates in age-associated diseases. More comprehensive recognition and understanding of the relationship between APC/C and ageing and age-related diseases will increase the development of targeted strategies for human health.
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Affiliation(s)
- Xiangdong Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiuling Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Correspondence: (X.C.); (B.L.)
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
- Correspondence: (X.C.); (B.L.)
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34
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Jacinto MP, Heidenreich D, Müller S, Greenberg MM. Covalent Modification of Bromodomain Proteins by Peptides Containing a DNA Damage-Induced, Histone Post-Translational Modification. Chembiochem 2022; 23:e202200373. [PMID: 36173930 PMCID: PMC9675715 DOI: 10.1002/cbic.202200373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/28/2022] [Indexed: 02/03/2023]
Abstract
An electrophilic 5-methylene-2-pyrrolone modification (KMP ) is produced at lysine residues of histone proteins in nucleosome core particles upon reaction with a commonly formed DNA lesion (C4-AP). The nonenzymatic KMP modification is also generated in the histones of HeLa cells treated with the antitumor agent, bleomycin that oxidizes DNA and forms C4-AP. This nonenzymatic covalent histone modification has the same charge as the N-acetyllysine (KAc ) modification but is more electrophilic. In this study we show that KMP -containing histone peptides are recognized by, and covalently modify bromodomain proteins that are KAc readers. Distinct selectivity preferences for covalent bromodomain modification are observed following incubation with KMP -containing peptides of different sequence. MS/MS analysis of 3 covalently modified bromodomain proteins confirmed that Cys adduction was selective. The modified Cys was not always proximal to the KAc binding site, indicating that KMP -containing peptide interaction with bromodomain protein is distinct from the former. Analysis of protein adduction yields as a function of bromodomain pH at which the protein charge is zero (pI) or cysteine solvent accessible surface area are also consistent with non-promiscuous interaction between the proteins and electrophilic peptides. These data suggest that intracellular formation of KMP could affect cellular function and viability by modifying proteins that regulate genetic expression.
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Affiliation(s)
- Marco Paolo Jacinto
- Chemistry, Johns Hopkins University, 3400 N. Charles St., 21218, Baltimore, MD, USA
| | - David Heidenreich
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Marc M Greenberg
- Chemistry, Johns Hopkins University, 3400 N. Charles St., 21218, Baltimore, MD, USA
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The oncogenic JAG1 intracellular domain is a transcriptional cofactor that acts in concert with DDX17/SMAD3/TGIF2. Cell Rep 2022; 41:111626. [DOI: 10.1016/j.celrep.2022.111626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/19/2022] [Accepted: 10/18/2022] [Indexed: 11/23/2022] Open
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36
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Zhang Q, Liu Y, Liao J, Wu R, Zhan Y, Zhang P, Luo S. Deficiency of p53 Causes the Inadequate Expression of miR-1246 in B Cells of Systemic Lupus Erythematosus. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1492-1498. [PMID: 36165173 PMCID: PMC9527209 DOI: 10.4049/jimmunol.2200307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/15/2022] [Indexed: 01/04/2023]
Abstract
Underexpression of p53 is considered the leading cause of the decreased miR-1246 expression in B cells of systemic lupus erythematosus (SLE) patients, yet the exact mechanism of action still remains unclear. To further explore the molecular mechanism of p53 upregulating miR-1246 expression, we targeted the methylation and acetylation of histone H3 in the miR-1246 promoter region of SLE B cells. We found that increased histone H3 trimethylation at Lys27 (H3K27me3) and decreased histone H3 acetylation at Lys9 and Lys14 (H3K9/K14ac) in the miR-1246 promoter region are essential for the low expression of miR-1246 in SLE B cells. p53 can promote miR-1246 transcription by recruiting Jumonji domain-containing protein 3 (JMJD3), E1A-binding protein p300 (EP300), and CREB-binding protein (CBP) to bind to the miR-1246 promoter, downregulating H3K27me3 and upregulating H3K9/K14ac. Furthermore, early B cell factor 1 (EBF1), CD40, CD38, and X box binding protein-1 (XBP-1) expression levels in SLE B cells transfected with p53 expression plasmid were significantly decreased, whereas autoantibody IgG production in autologous CD4+ T cells cocultured with overexpressed p53 SLE B cells was reduced. Collectively, our data suggest that the reduction of p53 decreases miR-1246 expression via upregulation of H3K27me3 and downregulation of H3K9/14ac, which in turn results in SLE B cell hyperactivity.
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Affiliation(s)
- Qing Zhang
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yu Liu
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jieyue Liao
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruifang Wu
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yi Zhan
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Peng Zhang
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuangyan Luo
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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Quaas CE, Lin B, Long DT. Transcription suppression is mediated by the HDAC1-Sin3 complex in Xenopus nucleoplasmic extract. J Biol Chem 2022; 298:102578. [PMID: 36220390 PMCID: PMC9650048 DOI: 10.1016/j.jbc.2022.102578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/24/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022] Open
Abstract
Modification of histones provides a dynamic mechanism to regulate chromatin structure and access to DNA. Histone acetylation, in particular, plays a prominent role in controlling the interaction between DNA, histones, and other chromatin-associated proteins. Defects in histone acetylation patterns interfere with normal gene expression and underlie a wide range of human diseases. Here, we utilize Xenopus egg extracts to investigate how changes in histone acetylation influence transcription of a defined gene construct. We show that inhibition of histone deacetylase 1 and 2 (HDAC1/2) specifically counteracts transcription suppression by preventing chromatin compaction and deacetylation of histone residues H4K5 and H4K8. Acetylation of these sites supports binding of the chromatin reader and transcription regulator BRD4. We also identify HDAC1 as the primary driver of transcription suppression and show that this activity is mediated through the Sin3 histone deacetylase complex. These findings highlight functional differences between HDAC1 and HDAC2, which are often considered to be functionally redundant, and provide additional molecular context for their activity.
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Tanemoto F, Nangaku M, Mimura I. Epigenetic memory contributing to the pathogenesis of AKI-to-CKD transition. Front Mol Biosci 2022; 9:1003227. [PMID: 36213117 PMCID: PMC9532834 DOI: 10.3389/fmolb.2022.1003227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Epigenetic memory, which refers to the ability of cells to retain and transmit epigenetic marks to their daughter cells, maintains unique gene expression patterns. Establishing programmed epigenetic memory at each stage of development is required for cell differentiation. Moreover, accumulating evidence shows that epigenetic memory acquired in response to environmental stimuli may be associated with diverse diseases. In the field of kidney diseases, the “memory” of acute kidney injury (AKI) leads to progression to chronic kidney disease (CKD); epidemiological studies show that patients who recover from AKI are at high risk of developing CKD. The underlying pathological processes include nephron loss, maladaptive epithelial repair, inflammation, and endothelial injury with vascular rarefaction. Further, epigenetic alterations may contribute as well to the pathophysiology of this AKI-to-CKD transition. Epigenetic changes induced by AKI, which can be recorded in cells, exert long-term effects as epigenetic memory. Considering the latest findings on the molecular basis of epigenetic memory and the pathophysiology of AKI-to-CKD transition, we propose here that epigenetic memory contributing to AKI-to-CKD transition can be classified according to the presence or absence of persistent changes in the associated regulation of gene expression, which we designate “driving” memory and “priming” memory, respectively. “Driving” memory, which persistently alters the regulation of gene expression, may contribute to disease progression by activating fibrogenic genes or inhibiting renoprotective genes. This process may be involved in generating the proinflammatory and profibrotic phenotypes of maladaptively repaired tubular cells after kidney injury. “Priming” memory is stored in seemingly successfully repaired tubular cells in the absence of detectable persistent phenotypic changes, which may enhance a subsequent transcriptional response to the second stimulus. This type of memory may contribute to AKI-to-CKD transition through the cumulative effects of enhanced expression of profibrotic genes required for wound repair after recurrent AKI. Further understanding of epigenetic memory will identify therapeutic targets of future epigenetic intervention to prevent AKI-to-CKD transition.
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Zeng C, Cheng TT, Ma X, Liu Y, Hua J, Chen X, Wang SY, Xu YJ. The absence of AhR in CD4 + T cells in patients with acute graft-versus-host disease may be related to insufficient CTCF expression. Clin Epigenetics 2022; 14:109. [PMID: 36056390 PMCID: PMC9440523 DOI: 10.1186/s13148-022-01330-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acute graft-versus-host disease (aGVHD) is a life-threatening complication of allogeneic hematopoietic stem cell transplantation (allo-HSCT). Accumulating evidence suggests that imbalanced Treg/Th17 ratio accelerates the progression of aGVHD. The aryl hydrocarbon receptor (AhR) is a basic helix-loop-helix transcription factor activated through cognate ligand binding. Current evidence supports that AhR plays a critical regulatory role in the differentiation of Treg and Th17 cells. However, the relationship between AhR and aGVHD remains unclear. RESULTS Our results showed that AhR expression was downregulated significantly in CD4+ T cells from patients with aGVHD compared with the non-aGVHD group. We also discovered that after activating AhR deficient CD4+ T cells, the expression levels of the activation markers-CD40L, CD134 and CD137 and cell proliferation activity were significantly higher than those of AhR-expressing CD4+ T cells. Restoring the expression of AhR in aGVHD CD4+ T cells resulted in significantly increased percentage of Tregs and associated gene transcripts, including Foxp3, IL-10 and CD39. In contrast, Th17 cell amounts and the transcription of related genes, including RORγt, IL-17A and IL-17F, were significantly reduced. We confirmed that CTCF recruited EP300 and TET2 to bind to the AhR promoter region and promoted AhR expression by mediating histone H3K9/K14 hyperacetylation and DNA demethylation in this region. The low expression of CTCF caused histone hypoacetylation and DNA hypermethylation of the AhR promoter, resulting in insufficient expression in aGVHD CD4+ T cells. CONCLUSIONS CTCF is an important inducer of AhR transcription. Insufficient expression of CTCF leads to excessive AhR downregulation, resulting in substantial CD4+ T cell activation and Th17/Treg ratio increase, thereby mediating the occurrence of aGVHD.
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Affiliation(s)
- Cong Zeng
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China.,Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
| | - Ting-Ting Cheng
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China.,Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
| | - Xia Ma
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China.,Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
| | - Yi Liu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China.,Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
| | - Juan Hua
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China.,Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
| | - Xu Chen
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China.,Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
| | - Shi-Yu Wang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China.,Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China
| | - Ya-Jing Xu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Diseases, Xiangya Hospital, Changsha, China. .,Hunan Hematology Oncology Clinical Medical Research Center, Changsha, China. .,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China.
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Zhang Y, Li Y, Zhang Y, Zhang Z, Zhang D, Wang X, Lai B, Huang D, Gu L, Xie Y, Miao Y. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4696-4715. [PMID: 35429161 DOI: 10.1093/jxb/erac155] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyun Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deyu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaonan Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binfan Lai
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dandan Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yakun Xie
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Lisi S, Trovato M, Vitaloni O, Fantini M, Chirichella M, Tognini P, Cornuti S, Costa M, Groth M, Cattaneo A. Acetylation-Specific Interference by Anti-Histone H3K9ac Intrabody Results in Precise Modulation of Gene Expression. Int J Mol Sci 2022; 23:ijms23168892. [PMID: 36012156 PMCID: PMC9408029 DOI: 10.3390/ijms23168892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/01/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
Among Histone post-translational modifications (PTMs), lysine acetylation plays a pivotal role in the epigenetic regulation of gene expression, mediated by chromatin modifying enzymes. Due to their activity in physiology and pathology, several chemical compounds have been developed to inhibit the function of these proteins. However, the pleiotropy of these classes of proteins represents a weakness of epigenetic drugs. Ideally, a new generation of epigenetic drugs should target with molecular precision individual acetylated lysines on the target protein. We exploit a PTM-directed interference, based on an intrabody (scFv-58F) that selectively binds acetylated lysine 9 of histone H3 (H3K9ac), to test the hypothesis that targeting H3K9ac yields more specific effects than inhibiting the corresponding HAT enzyme that installs that PTM. In yeast scFv-58F modulates, gene expression in a more specific way, compared to two well-established HAT inhibitors. This PTM-specific interference modulated expression of genes involved in ribosome biogenesis and function. In mammalian cells, the scFv-58F induces exclusive changes in the H3K9ac-dependent expression of specific genes. These results suggest the H3K9ac-specific intrabody as the founder of a new class of molecules to directly target histone PTMs, inverting the paradigm from inhibiting the writer enzyme to acting on the PTM.
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Affiliation(s)
- Simonetta Lisi
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
| | - Matteo Trovato
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | | | - Marco Fantini
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
| | | | - Paola Tognini
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Sara Cornuti
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
| | - Mario Costa
- Institute of Neurosciences, Consiglio Nazionale Delle Ricerche, 56124 Pisa, Italy
| | - Marco Groth
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, 56126 Pisa, Italy
- Correspondence: ; Tel.: +39-050-509320
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Lee U, Stuelsatz P, Karaz S, McKellar DW, Russeil J, Deak M, De Vlaminck I, Lepper C, Deplancke B, Cosgrove BD, Feige JN. A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle. iScience 2022; 25:104589. [PMID: 35789856 PMCID: PMC9250016 DOI: 10.1016/j.isci.2022.104589] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 03/10/2022] [Accepted: 06/08/2022] [Indexed: 11/23/2022] Open
Abstract
Apelin (Apln) is a myokine that regulates skeletal muscle plasticity and metabolism and declines during aging. Through a yeast one-hybrid transcription factor binding screen, we identified the TEA domain transcription factor 1 (Tead1) as a novel regulator of the Apln promoter. Single-cell analysis of regenerating muscle revealed that the apelin receptor (Aplnr) is enriched in endothelial cells, whereas Tead1 is enriched in myogenic cells. Knock-down of Tead1 stimulates Apln secretion from muscle cells in vitro and myofiber-specific overexpression of Tead1 suppresses Apln secretion in vivo. Apln secretion via Tead1 knock-down in muscle cells stimulates endothelial cell expansion via endothelial Aplnr. In vivo, Apln peptide supplementation enhances endothelial cell expansion while Tead1 muscle overexpression delays endothelial remodeling following muscle injury. Our work describes a novel paracrine crosstalk in which Apln secretion is controlled by Tead1 in myogenic cells and influences endothelial remodeling during muscle repair.
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Affiliation(s)
- Umji Lee
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pascal Stuelsatz
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Sonia Karaz
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - David W. McKellar
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Julie Russeil
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Maria Deak
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christoph Lepper
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Bart Deplancke
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Jerome N. Feige
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Xu Y, Miao Y, Tian X, Wang Q, Hu Y, Luo Q. Transcriptomic and Epigenomic Assessment Reveals Epigenetic Regulation of WRKY Genes in Response to Magnaporthe oryzae Infection in Rice. Curr Genomics 2022; 23:182-194. [PMID: 36777006 PMCID: PMC9878826 DOI: 10.2174/1389202923666220510195910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/07/2022] [Accepted: 03/28/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Histone acetylations acting as active hallmarks for gene transcription is involved in regulating numerous developmental and stress-responsive gene expression. Methods: The data from chromatin immunoprecipitation sequencing (ChIP-seq) was performed by using histone H3 lysine 9 acetylation (H3K9ac) antibody, and RNA sequencing (RNA-seq) utilizing rice seedlings inoculated by Magnaporthe oryzae (M. oryzae) were integrated. Results: RNA-seq data revealed that 422, 460 and 466 genes were up-regulated at 12h, 24h and 48h after inoculation. ChIP-seq data showed that 60%-80% of blast up-regulated genes at different time points were marked with H3K9ac, which was prone to be enriched in both TSS and gene body region. However, the H3K9ac level at a rather small proportion of the up-regulated genes was elevated after M. oryzae inoculation. We found that seven WRKY genes induced by rice blast fungus harbor H3K9ac. For different WRKY genes, blast fungus induction led to the increase of H3K9ac in distinct regions, including promoter, TSS or gene body, indicating that histone acetylation may play diverse roles in the activation of defense-related genes. By searching DNA-binding motifs of transcription factors in the promoter of genes with increased H3K9ac after M. oryzae infection, we found that ERF family protein-binding motifs were enriched with high -log P-value (>20), including ERF1, DEAR3, DREB2C, RAP2.6, RRTF1_3ARY, all of which contain GCC-box (GCCGCC). Conclusion: In this study, we revealed that the vast majority of genes induced by fungus M. oryzae were marked with H3K9ac preferring both TSS and gene body regions. However, H3K9ac enrichment was increased, responding to M. oryzae inoculation only at a low proportion of these genes, including several WRKY genes. Besides, for different genes, the increment of H3K9ac occurred in different regions. Finally, ERF proteins that have been proved to bind GCC-box might be one of the potential transcription factors for recruiting histone acetyltransferases to deposit histone acetylation at defense-related genes in rice.
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Affiliation(s)
- Yan Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education, Key Labo-ratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, 650201, Kunming, China;,College of Bioengineering, Jingchu University of Technology, 448000, Jingmen, China;,These authors contributed equally to this work.
| | - Yuanxin Miao
- College of Bioengineering, Jingchu University of Technology, 448000, Jingmen, China;,These authors contributed equally to this work.
| | - Xuejun Tian
- College of Bioengineering, Jingchu University of Technology, 448000, Jingmen, China
| | - Qihai Wang
- College of Bioengineering, Jingchu University of Technology, 448000, Jingmen, China
| | - Yongfeng Hu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, 443002, Yichang, Hubei, China,Address correspondence to these authors at the State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, 650201, Kunming, China; Tel/Fax: 13769133718; E-mail: and Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, 443002, Yichang, Hubei, China; Tel/Fax: 13677246318; E-mail:
| | - Qiong Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education, Key Labo-ratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, 650201, Kunming, China;,Address correspondence to these authors at the State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/Ministry of Education Key Laboratory of Agricultural Biodiversity for Plant Disease Management, Yunnan Agricultural University, 650201, Kunming, China; Tel/Fax: 13769133718; E-mail: and Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, 443002, Yichang, Hubei, China; Tel/Fax: 13677246318; E-mail:
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Shimizu J, Kawano F. Exercise-induced H3K27me3 facilitates the adaptation of skeletal muscle to exercise in mice. J Physiol 2022; 600:3331-3353. [PMID: 35666835 DOI: 10.1113/jp282917] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/30/2022] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Exercise mediates H3K27me3 at transcriptionally upregulated loci in skeletal muscle, although the role of H3K27me3 in the adaptation of skeletal muscle to exercise training is unclear. Chromatin immunoprecipitation followed by sequencing analysis demonstrated that H3K27me3, as well as H3K4me3 modifications, is the hallmark of sites showing higher responses to acute exercise. GSK343, a selective inhibitor of the enhancer of zeste homologue 2 (EZH2), enhanced the gene responses to a single bout of exercise and accelerated the adaptive changes during exercise training in association with myonuclear H3K27me3 accumulation. Administration of valemetostat, an EZH1/2 dual inhibitor, repressed myonuclear H3K27me3 accumulation during training and caused the failure in adaptive changes. Exercise-induced H3K27me3 may play a key role in inducing exercise-related effects in the skeletal muscle. ABSTRACT Histone H3 trimethylation at lysine 27 (H3K27me3) is known to act as a transcriptionally repressive histone modification via heterochromatin formation. However, in skeletal muscle, it was also reported that H3K27me3 was enriched at the sites transcriptionally activated by exercise, although the role of H3K27me3 in the adaptation to exercise is unknown. In this study, we first determined the genome-wide enrichment of RNA polymerase II and histone H3 trimethylation at lysine 4 (H3K4me3) and H3K27me3 using chromatin immunoprecipitation followed by sequencing analysis in mouse tibialis anterior muscle. The loci that were transcriptionally upregulated by a single bout of running exercise were marked by both H3K27me3 and H3K4me3, which also correlated with the distribution of RNA polymerase II. The genes that were not responsive to exercise exhibited high H3K4me3 occupancy, similar to the upregulated genes but with fewer H3K27me3. Next, we tested the effects of H3K27 methyltransferase, an enhancer of zeste homologue (EZH) 2-specific inhibitor GSK343. GSK343 administration unexpectedly enhanced the H3K27me3 occupancy at the target loci, leading to the upregulation of gene responses to acute exercise. GSK343 administration also facilitated the phenotypic transformation from IIb to IIa fibres and the upregulation of AMPK phosphorylation and HSP70, PDK4, PGC-1α, and MuRF1 levels. Furthermore, in contrast to the accelerated adaptation to exercise by GSK343, EZH1/2 dual inhibitor valemetostat administration caused the failure in the changes of the aforementioned parameters after exercise training. These results indicate that exercise-induced H3K27me3 plays a key role in inducing exercise-related effects in the skeletal muscle. Abstract figure legend The loci upregulated in response to exercise are characterized by a bivalent modification with histone H3 trimethylation at lysine 27 (H3K27me3) and lysine 4 (H3K4me3) in mouse skeletal muscle. Acute exercise further stimulates both H3K27me3 and H3K4me3 at these loci associated with the upregulation of gene transcription. Lysine methyltransferase EZH2-specific inhibitor GSK343 administration increased H3K27me3 and H3K4me3 occupancies at the target loci after a single bout of exercise. Chronic treatment of GSK343 during exercise training more upregulated H3K27me3 in muscle fibres. In addition, it increased the number of muscle fibres expressing type IIa myosin heavy chain (MyHC) and enhanced the adaptive changes in the related protein levels. In contrast, administration of valemetostat, an EZH1/2 dual inhibitor, decreased H3K27me3 and H3K4me3 occupancies after acute exercise and caused the failure in the exercise-induced effects after training. It was also suggested that EZH1 acted as a modifier of exercise-induced H3K27me3 in skeletal muscle. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Junya Shimizu
- Graduate School of Health Sciences, Matsumoto University, 2095-1 Niimura, Matsumoto City, Nagano, 390-1295, Japan
| | - Fuminori Kawano
- Graduate School of Health Sciences, Matsumoto University, 2095-1 Niimura, Matsumoto City, Nagano, 390-1295, Japan
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Dang Y, Li S, Zhao P, Xiao L, Wang L, Shi Y, Luo L, Wang S, Wang H, Zhang K. The lysine deacetylase activity of histone deacetylases 1 and 2 is required to safeguard zygotic genome activation in mice and cattle. Development 2022; 149:275603. [PMID: 35575026 DOI: 10.1242/dev.200854] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/03/2022] [Indexed: 12/15/2022]
Abstract
The genome is transcriptionally inert at fertilization and must be activated through a remarkable developmental process called zygotic genome activation (ZGA). Epigenetic reprogramming contributes significantly to the dynamic gene expression during ZGA; however, the mechanism has yet to be resolved. Here, we find histone deacetylases 1 and 2 (HDAC1/2) can regulate ZGA through lysine deacetylase activity. Notably, in mouse embryos, overexpression of a HDAC1/2 dominant-negative mutant leads to developmental arrest at the two-cell stage. RNA-seq reveals that 64% of downregulated genes are ZGA genes and 49% of upregulated genes are developmental genes. Inhibition of the deacetylase activity of HDAC1/2 causes a failure of histone deacetylation at multiple sites, including H4K5, H4K16, H3K14, H3K18 and H3K27. ChIP-seq analysis exhibits an increase and decrease of H3K27ac enrichment at promoters of up- and downregulated genes, respectively. Moreover, HDAC1 mutants prohibit the removal of H3K4me3 by impeding expression of Kdm5 genes. Importantly, the developmental block can be greatly rescued by Kdm5b injection and by partially correcting the expression of the majority of dysregulated genes. Similar functional significance of HDAC1/2 is conserved in bovine embryos. Overall, we propose that HDAC1/2 are indispensable for ZGA by creating correct transcriptional repressive and active states in mouse and bovine embryos.
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Affiliation(s)
- Yanna Dang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuang Li
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Panpan Zhao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lieying Xiao
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lefeng Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Department of Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Shi
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Luo
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohua Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huanan Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Department of Veterinary Sciences, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, and Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
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High-throughput profiling of histone post-translational modifications and chromatin modifying proteins by reverse phase protein array. J Proteomics 2022; 262:104596. [PMID: 35489683 PMCID: PMC10165948 DOI: 10.1016/j.jprot.2022.104596] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 03/23/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022]
Abstract
Epigenetic variation plays a significant role in normal development and human diseases including cancer, in part through post-translational modifications (PTMs) of histones. Identification and profiling of changes in histone PTMs, and in proteins regulating PTMs, are crucial to understanding diseases, and for discovery of epigenetic therapeutic agents. In this study, we have adapted and validated an antibody-based reverse phase protein array (RPPA) platform for profiling 20 histone PTMs and expression of 40 proteins that modify histones and other epigenomic regulators. The specificity of the RPPA assay for histone PTMs was validated with synthetic peptides corresponding to histone PTMs and by detection of histone PTM changes in response to inhibitors of histone modifier proteins in cell cultures. The useful application of the RPPA platform was demonstrated with two models: induction of pluripotent stem cells and a mouse mammary tumor progression model. Described here is a robust platform that includes a rapid microscale method for histone isolation and partially automated workflows for analysis of histone PTMs and histone modifiers that can be performed in a high-throughput manner with hundreds of samples. This RPPA platform has potential for translational applications through the discovery and validation of epigenetic states as therapeutic targets and biomarkers. SIGNIFICANCE: Our study has established an antibody-based reverse phase protein array platform for global profiling of a wide range of post-translational modifications of histones and histone modifier proteins. The high-throughput platform provides comprehensive analyses of epigenetics for biological research and disease studies and may serve as screening assay for diagnostic purpose or therapy development.
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Unveiling RCOR1 as a rheostat at transcriptionally permissive chromatin. Nat Commun 2022; 13:1550. [PMID: 35322029 PMCID: PMC8943175 DOI: 10.1038/s41467-022-29261-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2022] [Indexed: 12/23/2022] Open
Abstract
RCOR1 is a known transcription repressor that recruits and positions LSD1 and HDAC1/2 on chromatin to erase histone methylation and acetylation. However, there is currently an incomplete understanding of RCOR1’s range of localization and function. Here, we probe RCOR1’s distribution on a genome-wide scale and unexpectedly find that RCOR1 is predominantly associated with transcriptionally active genes. Biochemical analysis reveals that RCOR1 associates with RNA Polymerase II (POL-II) during transcription and deacetylates its carboxy-terminal domain (CTD) at lysine 7. We provide evidence that this non-canonical RCOR1 activity is linked to dampening of POL-II productive elongation at actively transcribing genes. Thus, RCOR1 represses transcription in two ways—first, via a canonical mechanism by erasing transcriptionally permissive histone modifications through associating with HDACs and, second, via a non-canonical mechanism that deacetylates RNA POL-II’s CTD to inhibit productive elongation. We conclude that RCOR1 is a transcription rheostat. The classical neuronal-gene corepressor RCOR1/CoREST is paradoxically enriched in transcriptionally active chromatin. Here the authors show RCOR1 is recruited during promoter-proximal pausing and negatively regulates the nascent-transcript synthesis. They also show that an RCOR1-LSD1- HDAC1 complex removes lysine acetylation from RNA polymerase II to repress transcription.
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Freeman B, White T, Kaul T, Stow EC, Baddoo M, Ungerleider N, Morales M, Yang H, Deharo D, Deininger P, Belancio V. Analysis of epigenetic features characteristic of L1 loci expressed in human cells. Nucleic Acids Res 2022; 50:1888-1907. [PMID: 35100410 PMCID: PMC8887483 DOI: 10.1093/nar/gkac013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 12/27/2021] [Accepted: 01/24/2022] [Indexed: 12/26/2022] Open
Abstract
Only a select few L1 loci in the human genome are expressed in any given cell line or organ, likely to minimize damage done to the genome. The epigenetic features and requirements of expressed L1 loci are currently unknown. Using human cells and comprehensive epigenetic analysis of individual expressed and unexpressed L1 loci, we determined that endogenous L1 transcription depends on a combination of epigenetic factors, including open chromatin, activating histone modifications, and hypomethylation at the L1 promoter. We demonstrate that the L1 promoter seems to require interaction with enhancer elements for optimal function. We utilize epigenetic context to predict the expression status of L1Hs loci that are poorly mappable with RNA-Seq. Our analysis identified a population of ‘transitional’ L1 loci that likely have greater potential to be activated during the epigenetic dysregulation seen in tumors and during aging because they are the most responsive to targeted CRISPR-mediated delivery of trans-activating domains. We demonstrate that an engineered increase in endogenous L1 mRNA expression increases Alu mobilization. Overall, our findings present the first global and comprehensive analysis of epigenetic status of individual L1 loci based on their expression status and demonstrate the importance of epigenetic context for L1 expression heterogeneity.
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Affiliation(s)
- Benjamin Freeman
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Travis White
- Sloan Kettering Institute for Cancer Research, NY, NY 10065, USA
| | - Tiffany Kaul
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Emily C Stow
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Melody Baddoo
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Maria Morales
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Hanlin Yang
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Dawn Deharo
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Prescott Deininger
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- To whom correspondence should be addressed. Tel: +1 504 988 4506; Fax: +1 504 988 1687;
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49
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Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals. Comput Struct Biotechnol J 2022; 20:353-367. [PMID: 35035788 PMCID: PMC8741409 DOI: 10.1016/j.csbj.2021.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/21/2022] Open
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50
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Abuhashem A, Garg V, Hadjantonakis AK. RNA polymerase II pausing in development: orchestrating transcription. Open Biol 2022; 12:210220. [PMID: 34982944 PMCID: PMC8727152 DOI: 10.1098/rsob.210220] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The coordinated regulation of transcriptional networks underpins cellular identity and developmental progression. RNA polymerase II promoter-proximal pausing (Pol II pausing) is a prevalent mechanism by which cells can control and synchronize transcription. Pol II pausing regulates the productive elongation step of transcription at key genes downstream of a variety of signalling pathways, such as FGF and Nodal. Recent advances in our understanding of the Pol II pausing machinery and its role in transcription call for an assessment of these findings within the context of development. In this review, we discuss our current understanding of the molecular basis of Pol II pausing and its function during organismal development. By critically assessing the tools used to study this process we conclude that combining recently developed genomics approaches with refined perturbation systems has the potential to expand our understanding of Pol II pausing mechanistically and functionally in the context of development and beyond.
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Affiliation(s)
- Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10021, USA,Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medical College, New York, NY 10021, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medical College, New York, NY 10021, USA
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