1
|
Rahman JF, Hoque H, Jubayer AA, Jewel NA, Hasan MN, Chowdhury AT, Prodhan SH. Alfin-like (AL) transcription factor family in Oryza sativa L.: Genome-wide analysis and expression profiling under different stresses. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 43:e00845. [PMID: 38962072 PMCID: PMC11217604 DOI: 10.1016/j.btre.2024.e00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/24/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024]
Abstract
Oryza sativa L. is the world's most essential and economically important food crop. Climate change and ecological imbalances make rice plants vulnerable to abiotic and biotic stresses, threatening global food security. The Alfin-like (AL) transcription factor family plays a crucial role in plant development and stress responses. This study comprehensively analyzed this gene family and their expression profiles in rice, revealing nine AL genes, classifying them into three distinct groups based on phylogenetic analysis and identifying four segmental duplication events. RNA-seq data analysis revealed high expression levels of OsALs in different tissues, growth stages, and their responsiveness to stresses. RT-qPCR data showed significant expression of OsALs in different abiotic stresses. Identification of potential cis-regulatory elements in promoter regions has also unveiled their involvement. Tertiary structures of the proteins were predicted. These findings would lay the groundwork for future research to reveal their molecular mechanism in stress tolerance and plant development.
Collapse
Affiliation(s)
- Jeba Faizah Rahman
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Hammadul Hoque
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Abdullah -Al- Jubayer
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Nurnabi Azad Jewel
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md. Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Aniqua Tasnim Chowdhury
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Shamsul H. Prodhan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| |
Collapse
|
2
|
Häußermann L, Singh A, Swart EC. Two paralogous PHD finger proteins participate in natural genome editing in Paramecium tetraurelia. J Cell Sci 2024; 137:jcs261979. [PMID: 39212120 PMCID: PMC11385659 DOI: 10.1242/jcs.261979] [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: 01/24/2024] [Accepted: 06/28/2024] [Indexed: 09/04/2024] Open
Abstract
The unicellular eukaryote Paramecium tetraurelia contains functionally distinct nuclei: germline micronuclei (MICs) and a somatic macronucleus (MAC). During sex, the MIC genome is reorganized into a new MAC genome and the old MAC is lost. Almost 45,000 unique internal eliminated sequences (IESs) distributed throughout the genome require precise excision to guarantee a functional new MAC genome. Here, we characterize a pair of paralogous PHD finger proteins involved in DNA elimination. DevPF1, the early-expressed paralog, is present in only some of the gametic and post-zygotic nuclei during meiosis. Both DevPF1 and DevPF2 localize in the new developing MACs, where IES excision occurs. Upon DevPF2 knockdown (KD), long IESs are preferentially retained and late-expressed small RNAs decrease; no length preference for retained IESs was observed in DevPF1-KD and development-specific small RNAs were abolished. The expression of at least two genes from the new MAC with roles in genome reorganization seems to be influenced by DevPF1- and DevPF2-KD. Thus, both PHD fingers are crucial for new MAC genome development, with distinct functions, potentially via regulation of non-coding and coding transcription in the MICs and new MACs.
Collapse
Affiliation(s)
- Lilia Häußermann
- Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Aditi Singh
- Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Estienne C Swart
- Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| |
Collapse
|
3
|
Dziulko AK, Allen H, Chuong EB. An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140. Hum Mol Genet 2024; 33:1454-1464. [PMID: 38751339 PMCID: PMC11305685 DOI: 10.1093/hmg/ddae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 07/26/2024] Open
Abstract
Speckled Protein 140 (SP140) is a chromatin reader with critical roles regulating immune cell transcriptional programs, and SP140 splice variants are associated with immune diseases including Crohn's disease, multiple sclerosis, and chronic lymphocytic leukemia. SP140 expression is currently thought to be restricted to immune cells. However, by analyzing human transcriptomic datasets from a wide range of normal and cancer cell types, we found recurrent cancer-specific expression of SP140, driven by an alternative intronic promoter derived from an intronic endogenous retrovirus (ERV). The ERV belongs to the primate-specific LTR8B family and is regulated by oncogenic mitogen-activated protein kinase (MAPK) signaling. The ERV drives expression of multiple cancer-specific isoforms, including a nearly full-length isoform that retains all the functional domains of the full-length canonical isoform and is also localized within the nucleus, consistent with a role in chromatin regulation. In a fibrosarcoma cell line, silencing the cancer-specific ERV promoter of SP140 resulted in increased sensitivity to interferon-mediated cytotoxicity and dysregulation of multiple genes. Our findings implicate aberrant ERV-mediated SP140 expression as a novel mechanism contributing to immune gene dysregulation in a wide range of cancer cells.
Collapse
Affiliation(s)
- Adam K Dziulko
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Holly Allen
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| |
Collapse
|
4
|
Ren Z, Tang H, Zhang W, Guo M, Cui J, Wang H, Xie B, Yu J, Chen Y, Zhang M, Han C, Chu T, Liang Q, Zhao S, Huang Y, He X, Liu K, Liu C, Chen C. The Role of KDM2A and H3K36me2 Demethylation in Modulating MAPK Signaling During Neurodevelopment. Neurosci Bull 2024; 40:1076-1092. [PMID: 38060137 PMCID: PMC11306490 DOI: 10.1007/s12264-023-01161-3] [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: 07/06/2023] [Accepted: 09/13/2023] [Indexed: 12/08/2023] Open
Abstract
Intellectual disability (ID) is a condition characterized by cognitive impairment and difficulties in adaptive functioning. In our research, we identified two de novo mutations (c.955C>T and c.732C>A) at the KDM2A locus in individuals with varying degrees of ID. In addition, by using the Gene4Denovo database, we discovered five additional cases of de novo mutations in KDM2A. The mutations we identified significantly decreased the expression of the KDM2A protein. To investigate the role of KDM2A in neural development, we used both 2D neural stem cell models and 3D cerebral organoids. Our findings demonstrated that the reduced expression of KDM2A impairs the proliferation of neural progenitor cells (NPCs), increases apoptosis, induces premature neuronal differentiation, and affects synapse maturation. Through ChIP-Seq analysis, we found that KDM2A exhibited binding to the transcription start site regions of genes involved in neurogenesis. In addition, the knockdown of KDM2A hindered H3K36me2 binding to the downstream regulatory elements of genes. By integrating ChIP-Seq and RNA-Seq data, we made a significant discovery of the core genes' remarkable enrichment in the MAPK signaling pathway. Importantly, this enrichment was specifically linked to the p38 MAPK pathway. Furthermore, disease enrichment analysis linked the differentially-expressed genes identified from RNA-Seq of NPCs and cerebral organoids to neurodevelopmental disorders such as ID, autism spectrum disorder, and schizophrenia. Overall, our findings suggest that KDM2A plays a crucial role in regulating the H3K36me2 modification of downstream genes, thereby modulating the MAPK signaling pathway and potentially impacting early brain development.
Collapse
Affiliation(s)
- Zongyao Ren
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Haiyan Tang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Wendiao Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Minghui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Jingjie Cui
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Children's Hospital, Changsha, 410007, China
| | - Bin Xie
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Jing Yu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Yonghao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Ming Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Cong Han
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Tianyao Chu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Qiuman Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Shunan Zhao
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Yingjie Huang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Xuelian He
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430014, China.
| | - Kefu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410011, China.
- Furong Laboratory, Changsha, 410000, China.
| |
Collapse
|
5
|
Guan Y, Gajewska J, Floryszak‐Wieczorek J, Tanwar UK, Sobieszczuk‐Nowicka E, Arasimowicz‐Jelonek M. Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology. MOLECULAR PLANT PATHOLOGY 2024; 25:e13497. [PMID: 39034655 PMCID: PMC11261156 DOI: 10.1111/mpp.13497] [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: 10/04/2023] [Revised: 06/21/2024] [Accepted: 07/02/2024] [Indexed: 07/23/2024]
Abstract
Phytophthora species are oomycetes that have evolved a broad spectrum of biological processes and improved strategies to cope with host and environmental challenges. A growing body of evidence indicates that the high pathogen plasticity is based on epigenetic regulation of gene expression linked to Phytophthora's rapid adjustment to endogenous cues and various stresses. As 5mC DNA methylation has not yet been identified in Phytophthora, the reversible processes of acetylation/deacetylation of histone proteins seem to play a pivotal role in the epigenetic control of gene expression in oomycetes. To explore this issue, we review the structure, diversity, and phylogeny of histone acetyltransferases (HATs) and histone deacetylases (HDACs) in six plant-damaging Phytophthora species: P. capsici, P. cinnamomi, P. infestans, P. parasitica, P. ramorum, and P. sojae. To further integrate and improve our understanding of the phylogenetic classification, evolutionary relationship, and functional characteristics, we supplement this review with a comprehensive view of HATs and HDACs using recent genome- and proteome-level databases. Finally, the potential functional role of transcriptional reprogramming mediated by epigenetic changes during Phytophthora species saprophytic and parasitic phases under nitro-oxidative stress is also briefly discussed.
Collapse
Affiliation(s)
- Yufeng Guan
- Department of Plant Ecophysiology, Institute of Experimental Biology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Joanna Gajewska
- Department of Plant Ecophysiology, Institute of Experimental Biology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | | | - Umesh Kumar Tanwar
- Department of Plant Physiology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Ewa Sobieszczuk‐Nowicka
- Department of Plant Physiology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Magdalena Arasimowicz‐Jelonek
- Department of Plant Ecophysiology, Institute of Experimental Biology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| |
Collapse
|
6
|
Zeppilli D, Madabeni A, Nogara PA, Rocha JBT, Orian L. Reactivity of Zinc Fingers in Oxidizing Environments: Insight from Molecular Models Through Activation Strain Analysis. Chempluschem 2024:e202400252. [PMID: 38842473 DOI: 10.1002/cplu.202400252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/07/2024]
Abstract
The reactivity of Zn2+ tetrahedral complexes with H2O2 was investigated in silico, as a first step in their disruption process. The substrates were chosen to represent the cores of three different zinc finger protein motifs, i. e., a Zn2+ ion coordinated to four cysteines (CCCC), to three cysteines and one histidine (CCCH), and to two cysteines and two histidines (CCHH). The cysteine and histidine ligands were further simplified to methyl thiolate and imidazole, respectively. H2O2 was chosen as an oxidizing agent due to its biological role as a metabolic product and species involved in signaling processes. The mechanism of oxidation of a coordinated cysteinate to sulfenate-κS and the trends for the different substrates were rationalized through activation strain analysis and energy decomposition analysis in the framework of scalar relativistic Density Functional Theory (DFT) calculations at ZORA-M06/TZ2P ae // ZORA-BLYP-D3(BJ)/TZ2P. CCCC is oxidized most easily, an outcome explained considering both electrostatic and orbital interactions. The isomerization to sulfenate-κO was attempted to assess whether this step may affect the ligand dissociation; however, it was found to introduce a kinetic barrier without improving the energetics of the dissociation. Lastly, ligand exchange with free thiolates and selenolates was investigated as a trigger for ligand dissociation, possibly leading to metal ejection; molecular docking simulations also support this hypothesis.
Collapse
Affiliation(s)
- Davide Zeppilli
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Andrea Madabeni
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Pablo A Nogara
- Departamento de Bioquímica e Biologia Molecolar, Universidade Federal de Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia Sul-rio-grandense (IFSul), Av. Leonel de Moura Brizola, 2501, 96418-400, Bagé, RS, Brasil
| | - João B T Rocha
- Departamento de Bioquímica e Biologia Molecolar, Universidade Federal de Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil
| | - Laura Orian
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| |
Collapse
|
7
|
Cao MX, Li SZ, Li HJ. MpMLO1 controls sperm discharge in liverwort. NATURE PLANTS 2024; 10:1027-1038. [PMID: 38831045 DOI: 10.1038/s41477-024-01703-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 04/18/2024] [Indexed: 06/05/2024]
Abstract
In bryophytes, sexual reproduction necessitates the release of motile sperm cells from a gametophyte into the environment. Since 1856, this process, particularly in liverworts, has been known to depend on water. However, the molecular mechanism underlying this phenomenon has remained elusive. Here we identify the plasma membrane protein MpMLO1 in Marchantia polymorpha, a model liverwort, as critical for sperm discharge from antheridia. The MpMLO1-expressing tip cells among the sperm-wrapping jacket cells undergo programmed cell death upon antheridium maturation to facilitate sperm discharge after the application of water and even hypertonic solutions. The absence of MpMLO1 leads to reduced cytoplasmic Ca2+ levels in tip cells, preventing cell death and consequently sperm discharge. Our findings reveal that MpMLO1-mediated programmed cell death in antheridial tip cells, regulated by cytosolic Ca2+ dynamics, is essential for sperm release, elucidating a key mechanism in bryophyte sexual reproduction and providing insights into terrestrial plant evolution.
Collapse
Affiliation(s)
- Meng-Xing Cao
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Center for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shi-Zhen Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Center for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Ju Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- Center for Molecular Agrobiology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
8
|
Li Y, Jiang Z, Xu Y, Yan J, Wu Q, Huang S, Wang L, Xie Y, Wu X, Wang Y, Li Y, Fan X, Li F, Yuan W. Pygo-F773W Mutation Reveals Novel Functions beyond Wnt Signaling in Drosophila. Int J Mol Sci 2024; 25:5998. [PMID: 38892188 PMCID: PMC11172468 DOI: 10.3390/ijms25115998] [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: 04/19/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Pygopus (Pygo) has been identified as a specific nuclear co-activator of the canonical Wingless (Wg)/Wnt signaling pathway in Drosophila melanogaster. Pygo proteins consist of two conserved domains: an N-terminal homologous domain (NHD) and a C-terminal plant homologous domain (PHD). The PHD's ability to bind to di- and trimethylated lysine 4 of histone H3 (H3K4me2/3) appears to be independent of Wnt signaling. There is ongoing debate regarding the significance of Pygo's histone-binding capacity. Drosophila Pygo orthologs have a tryptophan (W) > phenylalanine (F) substitution in their histone pocket-divider compared to vertebrates, leading to reduced histone affinity. In this research, we utilized CRISPR/Cas9 technology to introduce the Pygo-F773W point mutation in Drosophila, successfully establishing a viable homozygous Pygo mutant line for the first time. Adult mutant flies displayed noticeable abnormalities in reproduction, locomotion, heart function, and lifespan. RNA-seq and cluster analysis indicated that the mutation primarily affected pathways related to immunity, metabolism, and posttranslational modification in adult flies rather than the Wnt signaling pathway. Additionally, a reduction in H3K9 acetylation levels during the embryonic stage was observed in the mutant strains. These findings support the notion that Pygo plays a wider role in chromatin remodeling, with its involvement in Wnt signaling representing only a specific aspect of its chromatin-related functions.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Fang Li
- The Laboratory of Heart Development Research, College of Life Science, Hunan Normal University, Changsha 410081, China; (Y.L.); (Z.J.); (X.F.)
| | - Wuzhou Yuan
- The Laboratory of Heart Development Research, College of Life Science, Hunan Normal University, Changsha 410081, China; (Y.L.); (Z.J.); (X.F.)
| |
Collapse
|
9
|
Liu M, Li W, Zheng X, Yuan Z, Zhou Y, Yang J, Mao Y, Wang D, Wu Q, He Y, He L, Zong D, Chen J. Genome-Wide Identification and Expression Analysis of the PHD Finger Gene Family in Pea ( Pisum sativum). PLANTS (BASEL, SWITZERLAND) 2024; 13:1489. [PMID: 38891298 PMCID: PMC11174613 DOI: 10.3390/plants13111489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
The plant homeodomain finger (PHD finger) protein, a type of zinc finger protein extensively distributed in eukaryotes, plays diverse roles in regulating plant growth and development. While PHD finger proteins have been identified in various species, their functions remain largely unexplored in pea (Pisum sativum). In this study, we identified 84 members of the PHD finger gene family in pea, which displayed an uneven distribution across seven chromosomes. Through a comprehensive analysis using data from Arabidopsis thaliana and Medicago truncatula, we categorized the PHD finger proteins into 20 subfamilies via phylogenetic tree analysis. Each subfamily exhibited distinct variations in terms of quantity, genetic structure, conserved domains, and physical and chemical properties. Collinearity analysis revealed conserved evolutionary relationships among the PHD finger genes across the three different species. Furthermore, we identified the conserved and important roles of the subfamily M members in anther development. RT-qPCR and in situ hybridization revealed high expression of the pea subfamily M members PsPHD11 and PsPHD16 in microspores and the tapetum layer. In conclusion, this analysis of the PHD finger family in pea provides valuable guidance for future research on the biological roles of PHD finger proteins in pea and other leguminous plants.
Collapse
Affiliation(s)
- Mingli Liu
- School of Life Sciences, Southwest Forestry University, Kunming 650224, China; (M.L.); (W.L.)
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
| | - Wenju Li
- School of Life Sciences, Southwest Forestry University, Kunming 650224, China; (M.L.); (W.L.)
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
| | - Xiaoling Zheng
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Yuan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueqiong Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Yawen Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongfa Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Qing Wu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yexin He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
| | - Liangliang He
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Zong
- School of Life Sciences, Southwest Forestry University, Kunming 650224, China; (M.L.); (W.L.)
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (X.Z.); (Z.Y.); (Y.Z.); (J.Y.); (Y.M.); (D.W.); (Q.W.); (Y.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
10
|
Jung WJ, Jeong JH, Yoon JS, Seo YW. Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time. PLANT CELL REPORTS 2024; 43:142. [PMID: 38744747 DOI: 10.1007/s00299-024-03226-7] [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: 02/04/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE 111 PHD genes were newly identified in rye genome and ScPHD5's role in regulating cold tolerance and flowering time was suggested. Plant homeodomain (PHD)-finger proteins regulate the physical properties of chromatin and control plant development and stress tolerance. Although rye (Secale cereale L.) is a major winter crop, PHD-finger proteins in rye have not been studied. Here, we identified 111 PHD genes in the rye genome that exhibited diverse gene and protein sequence structures. Phylogenetic tree analysis revealed that PHDs were genetically close in monocots and diverged from those in dicots. Duplication and synteny analyses demonstrated that ScPHDs have undergone several duplications during evolution and that high synteny is conserved among the Triticeae species. Tissue-specific and abiotic stress-responsive gene expression analyses indicated that ScPHDs were highly expressed in spikelets and developing seeds and were responsive to cold and drought stress. One of these genes, ScPHD5, was selected for further functional characterization. ScPHD5 was highly expressed in the spike tissues and was localized in the nuclei of rye protoplasts and tobacco leaves. ScPHD5-overexpressing Brachypodium was more tolerant to freezing stress than wild-type (WT), with increased CBF and COR gene expression. Additionally, these transgenic plants displayed an extremely early flowering phenotype that flowered more than two weeks earlier than the WT, and vernalization genes, rather than photoperiod genes, were increased in the WT. RNA-seq analysis revealed that diverse stress response genes, including HSPs, HSFs, LEAs, and MADS-box genes, were also upregulated in transgenic plants. Our study will help elucidate the roles of PHD genes in plant development and abiotic stress tolerance in rye.
Collapse
Affiliation(s)
- Woo Joo Jung
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Korea
| | - Ji Hyeon Jeong
- Department of Plant Biotechnology, Korea University, Seoul, 02841, Korea
| | - Jin Seok Yoon
- Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul, 02841, Korea.
- Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, Korea.
| |
Collapse
|
11
|
Cui H, Zhu H, Ban W, Li Y, Chen R, Li L, Zhang X, Chen K, Xu H. Characterization of Two Gonadal Genes, zar1 and wt1b, in Hermaphroditic Fish Asian Seabass ( Lates calcarifer). Animals (Basel) 2024; 14:508. [PMID: 38338151 PMCID: PMC10854929 DOI: 10.3390/ani14030508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Zygote arrest-1 (Zar1) and Wilms' tumor 1 (Wt1) play an important role in oogenesis, with the latter also involved in testicular development and gender differentiation. Here, Lczar1 and Lcwt1b were identified in Asian seabass (Lates calcarifer), a hermaphrodite fish, as the valuable model for studying sex differentiation. The cloned cDNA fragments of Lczar1 were 1192 bp, encoding 336 amino acids, and contained a zinc-binding domain, while those of Lcwt1b cDNA were 1521 bp, encoding a peptide of 423 amino acids with a Zn finger domain belonging to Wt1b family. RT-qPCR analysis showed that Lczar1 mRNA was exclusively expressed in the ovary, while Lcwt1b mRNA was majorly expressed in the gonads in a higher amount in the testis than in the ovary. In situ hybridization results showed that Lczar1 mRNA was mainly concentrated in oogonia and oocytes at early stages in the ovary, but were undetectable in the testis. Lcwt1b mRNA was localized not only in gonadal somatic cells (the testis and ovary), but also in female and male germ cells in the early developmental stages, such as those of previtellogenic oocytes, spermatogonia, spermatocytes and spermatids. These results indicated that Lczar1 and Lcwt1b possibly play roles in gonadal development. Therefore, the findings of this study will provide a basis for clarifying the mechanism of Lczar1 and Lcwt1b in regulating germ cell development and the sex reversal of Asian seabass and even other hermaphroditic species.
Collapse
Affiliation(s)
- Han Cui
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Haoyu Zhu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Wenzhuo Ban
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Yulin Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Ruyi Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Lingli Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Xiaoling Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Kaili Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| | - Hongyan Xu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China; (H.C.); (H.Z.); (W.B.); (Y.L.); (R.C.); (L.L.); (X.Z.)
- Key Laboratory of Freshwater Fish Reproduction and Development, Chongqing 400715, China
- Key Laboratory of Aquatic Sciences of Chongqing, Ministry of Education, Chongqing 400715, China
| |
Collapse
|
12
|
Panahi B, Farhadian M, Hosseinzadeh Gharajeh N, Mohammadi SA, Hejazi MA. Meta-analysis of transcriptomic profiles in Dunaliella tertiolecta reveals molecular pathway responses to different abiotic stresses. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23002. [PMID: 38388445 DOI: 10.1071/fp23002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/04/2024] [Indexed: 02/24/2024]
Abstract
Microalgae are photosynthetic organisms and a potential source of sustainable metabolite production. However, different stress conditions might affect the production of various metabolites. In this study, a meta-analysis of RNA-seq experiments in Dunaliella tertiolecta was evaluated to compare metabolite biosynthesis pathways in response to abiotic stress conditions such as high light, nitrogen deficiency and high salinity. Results showed downregulation of light reaction, photorespiration, tetrapyrrole and lipid-related pathways occurred under salt stress. Nitrogen deficiency mostly induced the microalgal responses of light reaction and photorespiration metabolism. Phosphoenol pyruvate carboxylase, phosphoglucose isomerase, bisphosphoglycerate mutase and glucose-6-phosphate-1-dehydrogenase (involved in central carbon metabolism) were commonly upregulated under salt, light and nitrogen stresses. Interestingly, the results indicated that the meta-genes (modules of genes strongly correlated) were located in a hub of stress-specific protein-protein interaction (PPI) network. Module enrichment of meta-genes PPI networks highlighted the cross-talk between photosynthesis, fatty acids, starch and sucrose metabolism under multiple stress conditions. Moreover, it was observed that the coordinated expression of the tetrapyrrole intermediated with meta-genes was involved in starch biosynthesis. Our results also showed that the pathways of vitamin B6 metabolism, methane metabolism, ribosome biogenesis and folate biosynthesis responded specifically to different stress factors. Since the results of this study revealed the main pathways underlying the abiotic stress, they might be applied in optimised metabolite production by the microalga Dunaliella in future studies. PRISMA check list was also included in the study.
Collapse
Affiliation(s)
- Bahman Panahi
- Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
| | - Mohammad Farhadian
- Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany
| | | | | | - Mohammad Amin Hejazi
- Department of Food Biotechnology, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
| |
Collapse
|
13
|
Jin R, Yang H, Muhammad T, Li X, Tuerdiyusufu D, Wang B, Wang J. Involvement of Alfin-Like Transcription Factors in Plant Development and Stress Response. Genes (Basel) 2024; 15:184. [PMID: 38397174 PMCID: PMC10887727 DOI: 10.3390/genes15020184] [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: 01/02/2024] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Alfin-like (AL) proteins are an important class of transcription factor (TF) widely distributed in eukaryotes and play vital roles in many aspects of plant growth and development. AL proteins contain an Alfin-like domain and a specific PHD-finger structure domain at the N-terminus and C-terminus, respectively. The PHD domain can bind to a specific (C/A) CAC element in the promoter region and affect plant growth and development by regulating the expression of functional genes. This review describes a variety of AL transcription factors that have been isolated and characterized in Arabidopsis thaliana, Brassica rapa, Zea mays, Brassica oleracea, Solanum lycopersicum, Populus trichocarpa, Pyrus bretschenedri, Malus domestica, and other species. These studies have focused mainly on plant growth and development, different abiotic stress responses, different hormonal stress responses, and stress responses after exposure to pathogenic bacteria. However, studies on the molecular functional mechanisms of Alfin-like transcription factors and the interactions between different signaling pathways are rare. In this review, we performed phylogenetic analysis, cluster analysis, and motif analysis based on A. thaliana sequences. We summarize the structural characteristics of AL transcription factors in different plant species and the diverse functions of AL transcription factors in plant development and stress regulation responses. The aim of this study was to provide a reference for further application of the functions and mechanisms of action of the AL protein family in plants.
Collapse
Affiliation(s)
- Ruixin Jin
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (R.J.); (H.Y.); (T.M.); (X.L.); (D.T.)
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Haitao Yang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (R.J.); (H.Y.); (T.M.); (X.L.); (D.T.)
| | - Tayeb Muhammad
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (R.J.); (H.Y.); (T.M.); (X.L.); (D.T.)
| | - Xin Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (R.J.); (H.Y.); (T.M.); (X.L.); (D.T.)
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi 830052, China
| | - Diliaremu Tuerdiyusufu
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (R.J.); (H.Y.); (T.M.); (X.L.); (D.T.)
- College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi 830052, China
| | - Baike Wang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (R.J.); (H.Y.); (T.M.); (X.L.); (D.T.)
| | - Juan Wang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (R.J.); (H.Y.); (T.M.); (X.L.); (D.T.)
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| |
Collapse
|
14
|
Raux B, Buchan KA, Bennett J, Christott T, Dowling MS, Farnie G, Fedorov O, Gamble V, Gileadi C, Giroud C, Huber KVM, Korczynska M, Limberakis C, Narayanan A, Owen DR, Sáez LD, Stock IA, Londregan AT. Discovery of PFI-6, a small-molecule chemical probe for the YEATS domain of MLLT1 and MLLT3. Bioorg Med Chem Lett 2024; 98:129546. [PMID: 37944866 DOI: 10.1016/j.bmcl.2023.129546] [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: 08/31/2023] [Revised: 10/19/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Epigenetic proteins containing YEATS domains (YD) are an emerging target class in drug discovery. Described herein are the discovery and characterization efforts associated with PFI-6, a new chemical probe for the YD of MLLT1 (ENL/YEATS1) and MLLT3 (AF9/YEATS3). For hit identification, fragment-like mimetics of endogenous YD ligands (crotonylated histone-containing proteins), were synthesized via parallel medicinal chemistry (PMC) and screened for MLLT1 binding. Subsequent SAR studies led to iterative MLLT1/3 binding and selectivity improvements, culminating in the discovery of PFI-6. PFI-6 demonstrates good affinity and selectivity for MLLT1/3 vs. other human YD proteins (YEATS2/4) and engages MLLT3 in cells. Small-molecule X-ray co-crystal structures of two molecules, including PFI-6, bound to the YD of MLLT1/3 are also described. PFI-6 may be a useful tool molecule to better understand the biological effects associated with modulation of MLLT1/3.
Collapse
Affiliation(s)
- Brigitt Raux
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Karly A Buchan
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - James Bennett
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Thomas Christott
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | | | - Gillian Farnie
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Oleg Fedorov
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Vicki Gamble
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Carina Gileadi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Charline Giroud
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Kilian V M Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | | | - Chris Limberakis
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Arjun Narayanan
- Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA
| | - Dafydd R Owen
- Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA
| | - Laura Díaz Sáez
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Ingrid A Stock
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Allyn T Londregan
- Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA.
| |
Collapse
|
15
|
López-Garrido MP, Carrascosa-Romero MC, Montero-Hernández M, Ruiz-Almansa J, Sánchez-Sánchez F. Brief Report: Evidence of Autism Spectrum Disorder Caused by a Mutation in ATRX Gene: A Case Report. J Autism Dev Disord 2024; 54:379-388. [PMID: 35593993 DOI: 10.1007/s10803-022-05588-x] [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] [Accepted: 04/23/2022] [Indexed: 11/29/2022]
Abstract
ATRX mutations are commonly associated with alpha-thalassaemia mental retardation syndrome (ATR-X syndrome) with a notable variable expressivity. This X-linked disorder is characterized by intellectual disability (ID) in a higher or lesser degree, in which the alpha-thalassaemia feature is not always present. Other phenotypic manifestations like facial dimorphism, hypotonia, microcephaly, skeletal abnormalities or urogenital malformations have been frequently observed in ATR-X syndrome. Herein, we report a missense ATRX mutation (Thr1621Met) in a patient with an autism spectrum disorder (ASD) diagnosis. Except for ID, no typical signs of ATR-X syndrome were found in the patient. These results confirm the extensive phenotypic variability associated to ATRX mutations and show the involvement of this gene in the ASD.
Collapse
Affiliation(s)
- María-Pilar López-Garrido
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha (UCLM), Albacete, Spain
| | | | - Minerva Montero-Hernández
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha (UCLM), Albacete, Spain
| | - Jesús Ruiz-Almansa
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha (UCLM), Albacete, Spain
| | - Francisco Sánchez-Sánchez
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha (UCLM), Albacete, Spain.
| |
Collapse
|
16
|
Malik AH, Khurshaid N, Shabir N, Ashraf N. Transcriptome wide identification, characterization and expression analysis of PHD gene family in Crocus sativus. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:81-91. [PMID: 38435850 PMCID: PMC10902251 DOI: 10.1007/s12298-024-01410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 03/05/2024]
Abstract
Crocus sativus L., of the Iridaceae family, yields world's most prized spice, saffron. Saffron is well known for its distinctive aroma, odour and colour, which are imputed to the presence of some specific glycosylated apocarotenoids. Even though the main biosynthetic pathway and most of the enzymes leading to apocarotenoid production have been identified, the regulatory mechanisms that govern the developmental stage and tissue specific production of apocarotenoids in Crocus remain comparatively unravelled. Towards this, we report identification, and characterization of plant homeodomain (PHD) finger transcription factor family in Crocus sativus. We also report cloning and characterisation of CstPHD27 from C. sativus. CstPHD27 recorded highest expression in stigma throughout flower development. CstPHD27 exhibited expression pattern which corresponded to the apocarotenoid accumulation in Crocus stigmas. CstPHD27 is nuclear localized and transcriptionally active in yeast Y187 strain. Over-expression of CstPHD27 in Crocus stigmas enhanced apocarotenoid content by upregulating the biosynthetic pathway genes. This report on PHD finger transcription factor family from C. sativus may offer a basis for elucidating role of this gene family in this traditionally and industrially prized crop. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01410-3.
Collapse
Affiliation(s)
- Aubid Hussain Malik
- Plant Molecular Biology and Biotechnology Division, CSIR—Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, Jammu and Kashmir 190005 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Nargis Khurshaid
- Plant Molecular Biology and Biotechnology Division, CSIR—Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, Jammu and Kashmir 190005 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Najwa Shabir
- Plant Molecular Biology and Biotechnology Division, CSIR—Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, Jammu and Kashmir 190005 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Nasheeman Ashraf
- Plant Molecular Biology and Biotechnology Division, CSIR—Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, Jammu and Kashmir 190005 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| |
Collapse
|
17
|
Lee HS, Bang I, You J, Jeong TK, Kim CR, Hwang M, Kim JS, Baek SH, Song JJ, Choi HJ. Molecular basis for PHF7-mediated ubiquitination of histone H3. Genes Dev 2023; 37:984-997. [PMID: 37993255 PMCID: PMC10760634 DOI: 10.1101/gad.350989.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
The RING-type E3 ligase has been known for over two decades, yet its diverse modes of action are still the subject of active research. Plant homeodomain (PHD) finger protein 7 (PHF7) is a RING-type E3 ubiquitin ligase responsible for histone ubiquitination. PHF7 comprises three zinc finger domains: an extended PHD (ePHD), a RING domain, and a PHD. While the function of the RING domain is largely understood, the roles of the other two domains in E3 ligase activity remain elusive. Here, we present the crystal structure of PHF7 in complex with the E2 ubiquitin-conjugating enzyme (E2). Our structure shows that E2 is effectively captured between the RING domain and the C-terminal PHD, facilitating E2 recruitment through direct contact. In addition, through in vitro binding and functional assays, we demonstrate that the N-terminal ePHD recognizes the nucleosome via DNA binding, whereas the C-terminal PHD is involved in histone H3 recognition. Our results provide a molecular basis for the E3 ligase activity of PHF7 and uncover the specific yet collaborative contributions of each domain to the PHF7 ubiquitination activity.
Collapse
Affiliation(s)
- Hyun Sik Lee
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Injin Bang
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, New York 10016, USA
| | - Junghyun You
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Tae-Kyeong Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Chang Rok Kim
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Minsang Hwang
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jong-Seo Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Hee Baek
- Creative Research Initiatives Center for Epigenetic Code and Diseases, School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea;
| |
Collapse
|
18
|
Rafiq Mohammed A, Assad D, Rostami G, Hamid M. Frequency and prognostic influence of ASXL1 mutations and its potential association with BCR-ABL1 transcript type and smoke in chronic myeloid leukemia patients. Gene 2023; 886:147776. [PMID: 37689224 DOI: 10.1016/j.gene.2023.147776] [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: 05/02/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/11/2023]
Abstract
BACKGROUND Heterogeneous response to tyrosine kinase inhibitors (TKIs) and progress to advance phases, still is a significant clinical problem. These are attributed to additional mutations in mutated non-ABL1 genes. we aimed to determine prognostic effects of ASXL1 mutations as a biomarker for diverse treatment response and disease progression to aid clinical management. METHODS We performed ASXL1 gene mutational screening in 80 Ph+CML patients at different phases and 10 healthy control by direct sequencing method. Multiplex and qRT-PCR, standard chromosome banding analysis were used to determine BCR-ABL1 transcript type, molecular and cytogenetic responses respectively. RESULTS overall, four type mutations were identified in 11.25% of the patients. There was significant difference regarding mutation frequency between chronic and advance phases (P = 0.0002), sokal risk score (P = 0.0001), smoking (P = 0.02) and mean of during time of imatinib treatment (P = 0.009) between patients with and without ASXL1 mutations. ASXL1 mutations frequency had a bias toward younger than older and women than men, but no significant (P > 0.05). ASXL1 mutations were found more recurrently in patients carrying ABL1 KD mutations (P = 0.003). The risk of increasing resistance and disease progression in patients with ASXL1 mutations was 32 and 63 fold higher than those without mutations respectively (P = 0.01; P = 0.0002). The risk of ASXL1 mutations presence in patients with b2a2 transcript type was much higher than b3a2 type (P = 0.02, OR = 10). CONCLUSION Our findings suggest that ASXL1 mutations may be favorable predictive biomarkers to determine the best TKI for each patient, and to prevent CML progression.
Collapse
Affiliation(s)
- Aras Rafiq Mohammed
- Department of Biology, College of Science, Sulaimani University, Sulaymanyah, Iraq
| | - Dlnya Assad
- Department of Biology, College of Science, Sulaimani University, Sulaymanyah, Iraq
| | - Golale Rostami
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Hamid
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
19
|
Quan W, Chan Z, Wei P, Mao Y, Bartels D, Liu X. PHD finger proteins function in plant development and abiotic stress responses: an overview. FRONTIERS IN PLANT SCIENCE 2023; 14:1297607. [PMID: 38046601 PMCID: PMC10693458 DOI: 10.3389/fpls.2023.1297607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
The plant homeodomain (PHD) finger with a conserved Cys4-His-Cys3 motif is a common zinc-binding domain, which is widely present in all eukaryotic genomes. The PHD finger is the "reader" domain of methylation marks in histone H3 and plays a role in the regulation of gene expression patterns. Numerous proteins containing the PHD finger have been found in plants. In this review, we summarize the functional studies on PHD finger proteins in plant growth and development and responses to abiotic stresses in recent years. Some PHD finger proteins, such as VIN3, VILs, and Ehd3, are involved in the regulation of flowering time, while some PHD finger proteins participate in the pollen development, for example, MS, TIP3, and MMD1. Furthermore, other PHD finger proteins regulate the plant tolerance to abiotic stresses, including Alfin1, ALs, and AtSIZ1. Research suggests that PHD finger proteins, as an essential transcription regulator family, play critical roles in various plant biological processes, which is helpful in understanding the molecular mechanisms of novel PHD finger proteins to perform specific function.
Collapse
Affiliation(s)
- Wenli Quan
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, China
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Zhulong Chan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Piwei Wei
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, China
| | - Yahui Mao
- College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Xun Liu
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin, China
| |
Collapse
|
20
|
Ngubo M, Moradi F, Ito CY, Stanford WL. Tissue-Specific Tumour Suppressor and Oncogenic Activities of the Polycomb-like Protein MTF2. Genes (Basel) 2023; 14:1879. [PMID: 37895228 PMCID: PMC10606531 DOI: 10.3390/genes14101879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
The Polycomb repressive complex 2 (PRC2) is a conserved chromatin-remodelling complex that catalyses the trimethylation of histone H3 lysine 27 (H3K27me3), a mark associated with gene silencing. PRC2 regulates chromatin structure and gene expression during organismal and tissue development and tissue homeostasis in the adult. PRC2 core subunits are associated with various accessory proteins that modulate its function and recruitment to target genes. The multimeric composition of accessory proteins results in two distinct variant complexes of PRC2, PRC2.1 and PRC2.2. Metal response element-binding transcription factor 2 (MTF2) is one of the Polycomb-like proteins (PCLs) that forms the PRC2.1 complex. MTF2 is highly conserved, and as an accessory subunit of PRC2, it has important roles in embryonic stem cell self-renewal and differentiation, development, and cancer progression. Here, we review the impact of MTF2 in PRC2 complex assembly, catalytic activity, and spatiotemporal function. The emerging paradoxical evidence suggesting that MTF2 has divergent roles as either a tumour suppressor or an oncogene in different tissues merits further investigations. Altogether, our review illuminates the context-dependent roles of MTF2 in Polycomb group (PcG) protein-mediated epigenetic regulation. Its impact on disease paves the way for a deeper understanding of epigenetic regulation and novel therapeutic strategies.
Collapse
Affiliation(s)
- Mzwanele Ngubo
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Fereshteh Moradi
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Caryn Y. Ito
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - William L. Stanford
- The Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| |
Collapse
|
21
|
Wen J, Deng M, Zhao K, Zhou H, Wu R, Li M, Cheng H, Li P, Zhang R, Lv J. Characterization of Plant Homeodomain Transcription Factor Genes Involved in Flower Development and Multiple Abiotic Stress Response in Pepper. Genes (Basel) 2023; 14:1737. [PMID: 37761877 PMCID: PMC10531376 DOI: 10.3390/genes14091737] [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: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Plant homeodomain (PHD) transcription factor genes are involved in plant development and in a plant's response to stress. However, there are few reports about this gene family in peppers (Capsicum annuum L.). In this study, the pepper inbred line "Zunla-1" was used as the reference genome, and a total of 43 PHD genes were identified, and systematic analysis was performed to study the chromosomal location, evolutionary relationship, gene structure, domains, and upstream cis-regulatory elements of the CaPHD genes. The fewest CaPHD genes were located on chromosome 4, while the most were on chromosome 3. Genes with similar gene structures and domains were clustered together. Expression analysis showed that the expression of CaPHD genes was quite different in different tissues and in response to various stress treatments. The expression of CaPHD17 was different in the early stage of flower bud development in the near-isogenic cytoplasmic male-sterile inbred and the maintainer inbred lines. It is speculated that this gene is involved in the development of male sterility in pepper. CaPHD37 was significantly upregulated in leaves and roots after heat stress, and it is speculated that CaPHD37 plays an important role in tolerating heat stress in pepper; in addition, CaPHD9, CaPHD10, CaPHD11, CaPHD17, CaPHD19, CaPHD20, and CaPHD43 were not sensitive to abiotic stress or hormonal factors. This study will provide the basis for further research into the function of CaPHD genes in plant development and responses to abiotic stresses and hormones.
Collapse
Affiliation(s)
- Jinfen Wen
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650500, China;
| | - Minghua Deng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Kai Zhao
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Huidan Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Rui Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Mengjuan Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Hong Cheng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Pingping Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Ruihao Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| | - Junheng Lv
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (M.D.); (K.Z.); (H.Z.); (R.W.); (M.L.); (H.C.); (P.L.); (R.Z.)
| |
Collapse
|
22
|
Cheng M, Cao H, Yao P, Guan J, Wu P, Ji H, Jiang S, Yuan Y, Fu L, Zheng Q, Li Q. PHF23 promotes NSCLC proliferation, metastasis, and chemoresistance via stabilization of ACTN4 and activation of the ERK pathway. Cell Death Dis 2023; 14:558. [PMID: 37626047 PMCID: PMC10457402 DOI: 10.1038/s41419-023-06069-4] [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: 04/17/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023]
Abstract
At present, non-small cell lung cancer (NSCLC) is still one of the leading causes of cancer-related deaths. Chemotherapy remains the standard treatment for NSCLC. However, the emergence of chemoresistance is one of the major obstacles to lung cancer treatment. Plant homologous structural domain finger protein 23 (PHF23) plays crucial roles in multiple cell fates. However, the clinical significance and biological role of PHF23 in NSCLC remain elusive. The Cancer Genome Atlas data mining, NCBI/GEO data mining, and western blotting analysis were employed to characterize the expression of PHF23 in NSCLC cell lines and tissues. Statistical analysis of immunohistochemistry and the Kaplan-Meier Plotter database were used to investigate the clinical significance of PHF23. A series of in vivo and in vitro assays, including assays for colony formation, cell viability, 5-ethynyl-2'-deoxyuridine (EDU incorporation) and Transwell migration, flow cytometry, RT-PCR, gene set enrichment analysis, co-immunoprecipitation analysis, and a xenograft tumor model, were performed to demonstrate the effects of PHF23 on the chemosensitivity of NSCLC cells and to clarify the underlying molecular mechanisms. PHF23 is overexpressed in NSCLC cell lines and tissues. High PHF23 levels correlate with short survival times and a poor response to chemotherapy in NSCLC patients. PHF23 overexpression facilitates cell proliferation, migration and sensitizes NSCLC cells to Cisplatin and Docetaxel by promoting DNA damage repair. Alpha-actinin-4 (ACTN4), as a downstream regulator, interacts with PHD domain of PHF23. Moreover, PHF23 is involved in ACTN4 stabilization by inhibiting its ubiquitination level. These results show that PHF23 plays an important role in the development and progression of NSCLC and suggest that PHF23 may serve as a therapeutic target in NSCLC patients.
Collapse
Affiliation(s)
- Ming Cheng
- Department of Pathology, College of Basic Medical Sciences, China Medical University, 110000, Shenyang, Liaoning Province, People's Republic of China
| | - Hongyi Cao
- Department of Pathology, College of Basic Medical Sciences, China Medical University, 110000, Shenyang, Liaoning Province, People's Republic of China
- Department of Pathology, The First Hospital of China Medical University, No. 155 NanjingBei Street, Heping District, 110000, Shenyang, Liaoning Province, People's Republic of China
| | - Peifeng Yao
- Department of Hand Surgery, Central Hospital affiliated to Shenyang Medical College, 110000, Shenyang, Liaoning Province, People's Republic of China
| | - Jingqian Guan
- Department of Pathology, College of Basic Medical Sciences, China Medical University, 110000, Shenyang, Liaoning Province, People's Republic of China
| | - Peihong Wu
- Department of Pathology, College of Basic Medical Sciences, China Medical University, 110000, Shenyang, Liaoning Province, People's Republic of China
| | - Hairu Ji
- Department of Pathology, Chengde Medical University, 067000, Chengde, Hebei Province, People's Republic of China
| | - Siyu Jiang
- Department of Pathology, College of Basic Medical Sciences, China Medical University, 110000, Shenyang, Liaoning Province, People's Republic of China
| | - Yinan Yuan
- Department of Pathology, College of Basic Medical Sciences, China Medical University, 110000, Shenyang, Liaoning Province, People's Republic of China
| | - Lin Fu
- Department of Pathology, College of Basic Medical Sciences, China Medical University, 110000, Shenyang, Liaoning Province, People's Republic of China.
- Department of Pathology, The First Hospital of China Medical University, No. 155 NanjingBei Street, Heping District, 110000, Shenyang, Liaoning Province, People's Republic of China.
| | - Qianqian Zheng
- Department of Pathophysiology, College of Basic Medical Sciences, China Medical University, 110000, Shenyang, Liaoning Province, People's Republic of China.
| | - Qingchang Li
- Department of Pathology, College of Basic Medical Sciences, China Medical University, 110000, Shenyang, Liaoning Province, People's Republic of China.
- Department of Pathology, The First Hospital of China Medical University, No. 155 NanjingBei Street, Heping District, 110000, Shenyang, Liaoning Province, People's Republic of China.
| |
Collapse
|
23
|
Wang J, Sun Z, Liu H, Yue L, Wang F, Liu S, Su B, Liu B, Kong F, Fang C. Genome-Wide Identification and Characterization of the Soybean Snf2 Gene Family and Expression Response to Rhizobia. Int J Mol Sci 2023; 24:ijms24087250. [PMID: 37108411 PMCID: PMC10138738 DOI: 10.3390/ijms24087250] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Sucrose nonfermenting 2 (Snf2) family proteins are the core component of chromatin remodeling complexes that can alter chromatin structure and nucleosome position by utilizing the energy of ATP, playing a vital role in transcription regulation, DNA replication, and DNA damage repair. Snf2 family proteins have been characterized in various species including plants, and they have been found to regulate development and stress responses in Arabidopsis. Soybean (Glycine max) is an important food and economic crop worldwide, unlike other non-leguminous crops, soybeans can form a symbiotic relationship with rhizobia for biological nitrogen fixation. However, little is known about Snf2 family proteins in soybean. In this study, we identified 66 Snf2 family genes in soybean that could be classified into six groups like Arabidopsis, unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis with Arabidopsis revealed that these 66 Snf2 family genes could be divided into 18 subfamilies. Collinear analysis showed that segmental duplication was the main mechanism for expansion of Snf2 genes rather than tandem repeats. Further evolutionary analysis indicated that the duplicated gene pairs had undergone purifying selection. All Snf2 proteins contained seven domains, and each Snf2 protein had at least one SNF2_N domain and one Helicase_C domain. Promoter analysis revealed that most Snf2 genes had cis-elements associated with jasmonic acid, abscisic acid, and nodule specificity in their promoter regions. Microarray data and real-time quantitative PCR (qPCR) analysis revealed that the expression profiles of most Snf2 family genes were detected in both root and nodule tissues, and some of them were found to be significantly downregulated after rhizobial infection. In this study, we conducted a comprehensive analysis of the soybean Snf2 family genes and demonstrated their responsiveness to Rhizobia infection. This provides insight into the potential roles of Snf2 family genes in soybean symbiotic nodulation.
Collapse
Affiliation(s)
- Jianhao Wang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhihui Sun
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Huan Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Lin Yue
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Fan Wang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Shuangrong Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Bohong Su
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Baohui Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Fanjiang Kong
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Chao Fang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| |
Collapse
|
24
|
Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JM, Dadras A, Zegers JM, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ari JB, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526407. [PMID: 36778228 PMCID: PMC9915684 DOI: 10.1101/2023.01.31.526407] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains of Zygnema circumcarinatum and one strain of Z. cylindricum) and generated chromosome-scale assemblies for all strains of the emerging model system Z. circumcarinatum. Comparative genomic analyses reveal expanded genes for signaling cascades, environmental response, and intracellular trafficking that we associate with multicellularity. Gene family analyses suggest that Zygnematophyceae share all the major enzymes with land plants for cell wall polysaccharide synthesis, degradation, and modifications; most of the enzymes for cell wall innovations, especially for polysaccharide backbone synthesis, were gained more than 700 million years ago. In Zygnematophyceae, these enzyme families expanded, forming co-expressed modules. Transcriptomic profiling of over 19 growth conditions combined with co-expression network analyses uncover cohorts of genes that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
Collapse
Affiliation(s)
- Xuehuan Feng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Jinfang Zheng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Iker Irisarri
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Huihui Yu
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
| | - Bo Zheng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Zahin Ali
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Sophie de Vries
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Janine M.R. Fürst-Jansen
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Armin Dadras
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Jaccoline M.S. Zegers
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tim P. Rieseberg
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Amra Dhabalia Ashok
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Maaike J. Bierenbroodspot
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Lydia Gramzow
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - Romy Petroll
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B. Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (UMA-CSIC)
| | - Orestis Nousias
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Tang Li
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Elisabeth Fitzek
- Computational Biology, Department of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - W. Scott Grayburn
- Northern Illinois University, Molecular Core Lab, Department of Biological Sciences, DeKalb, IL 60115, USA
| | - Nina Rittmeier
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Charlotte Permann
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Florian Rümpler
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - John M. Archibald
- Dalhousie University, Department of Biochemistry and Molecular Biology, 5850 College Street, Halifax NS B3H 4R2, Canada
| | - Günter Theißen
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - Jeffrey P. Mower
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
| | - Maike Lorenz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae at Goettingen University (EPSAG), Nikolausberger Weg 18, 37073 Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Technikumplatz 17, 09648 Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Lori Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard D. Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Xiyin Wang
- North China University of Science and Technology
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Cornell University, Plant Biology Section, Ithaca, NY, USA
| | - Stefan A. Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- University of Freiburg, Centre for Biological Signalling Studies (BIOSS), Freiburg, Germany
| | - Julius Ben Ari
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Noa Keren
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Assaf Mosquna
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Andreas Holzinger
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Chi Zhang
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, NE 68588, USA
| | - Jinling Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Marek Mutwil
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jan de Vries
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Yanbin Yin
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| |
Collapse
|
25
|
Londregan AT, Aitmakhanova K, Bennett J, Byrnes LJ, Canterbury DP, Cheng X, Christott T, Clemens J, Coffey SB, Dias JM, Dowling MS, Farnie G, Fedorov O, Fennell KF, Gamble V, Gileadi C, Giroud C, Harris MR, Hollingshead BD, Huber K, Korczynska M, Lapham K, Loria PM, Narayanan A, Owen DR, Raux B, Sahasrabudhe PV, Ruggeri RB, Sáez LD, Stock IA, Thuma BA, Tsai A, Varghese AE. Discovery of High-Affinity Small-Molecule Binders of the Epigenetic Reader YEATS4. J Med Chem 2023; 66:460-472. [PMID: 36562986 DOI: 10.1021/acs.jmedchem.2c01421] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A series of small-molecule YEATS4 binders have been discovered as part of an ongoing research effort to generate high-quality probe molecules for emerging and/or challenging epigenetic targets. Analogues such as 4d and 4e demonstrate excellent potency and selectivity for YEATS4 binding versus YEATS1,2,3 and exhibit good physical properties and in vitro safety profiles. A new X-ray crystal structure confirms direct binding of this chemical series to YEATS4 at the lysine acetylation recognition site of the YEATS domain. Multiple analogues engage YEATS4 with nanomolar potency in a whole-cell nanoluciferase bioluminescent resonance energy transfer assay. Rodent pharmacokinetic studies demonstrate the competency of several analogues as in vivo-capable binders.
Collapse
Affiliation(s)
- Allyn T Londregan
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | | | - James Bennett
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Laura J Byrnes
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Daniel P Canterbury
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Xiayun Cheng
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Thomas Christott
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Jennifer Clemens
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Steven B Coffey
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - João M Dias
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Matthew S Dowling
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Gillian Farnie
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Kimberly F Fennell
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Vicki Gamble
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Carina Gileadi
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Charline Giroud
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Michael R Harris
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Brett D Hollingshead
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Kilian Huber
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Magdalena Korczynska
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Kimberly Lapham
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Paula M Loria
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Arjun Narayanan
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Dafydd R Owen
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Brigitt Raux
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Parag V Sahasrabudhe
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Roger B Ruggeri
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Laura Díaz Sáez
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Ingrid A Stock
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Benjamin A Thuma
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Andy Tsai
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Alison E Varghese
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| |
Collapse
|
26
|
Stroynowska-Czerwinska AM, Klimczak M, Pastor M, Kazrani AA, Misztal K, Bochtler M. Clustered PHD domains in KMT2/MLL proteins are attracted by H3K4me3 and H3 acetylation-rich active promoters and enhancers. Cell Mol Life Sci 2023; 80:23. [PMID: 36598580 PMCID: PMC9813062 DOI: 10.1007/s00018-022-04651-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 01/05/2023]
Abstract
Histone lysine-specific methyltransferase 2 (KMT2A-D) proteins, alternatively called mixed lineage leukemia (MLL1-4) proteins, mediate positive transcriptional memory. Acting as the catalytic subunits of human COMPASS-like complexes, KMT2A-D methylate H3K4 at promoters and enhancers. KMT2A-D contain understudied highly conserved triplets and a quartet of plant homeodomains (PHDs). Here, we show that all clustered (multiple) PHDs localize to the well-defined loci of H3K4me3 and H3 acetylation-rich active promoters and enhancers. Surprisingly, we observe little difference in binding pattern between PHDs from promoter-specific KMT2A-B and enhancer-specific KMT2C-D. Fusion of the KMT2A CXXC domain to the PHDs drastically enhances their preference for promoters over enhancers. Hence, the presence of CXXC domains in KMT2A-B, but not KMT2C-D, may explain the promoter/enhancer preferences of the full-length proteins. Importantly, targets of PHDs overlap with KMT2A targets and are enriched in genes involved in the cancer pathways. We also observe that PHDs of KMT2A-D are mutated in cancer, especially within conserved folding motifs (Cys4HisCys2Cys/His). The mutations cause a domain loss-of-function. Taken together, our data suggest that PHDs of KMT2A-D guide the full-length proteins to active promoters and enhancers, and thus play a role in positive transcriptional memory.
Collapse
Affiliation(s)
| | - Magdalena Klimczak
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
| | - Michal Pastor
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Asgar Abbas Kazrani
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Katarzyna Misztal
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland.
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland.
| |
Collapse
|
27
|
Wen H, Shi X. Histone Readers and Their Roles in Cancer. Cancer Treat Res 2023; 190:245-272. [PMID: 38113004 PMCID: PMC11395558 DOI: 10.1007/978-3-031-45654-1_8] [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: 12/21/2023]
Abstract
Histone proteins in eukaryotic cells are subjected to a wide variety of post-translational modifications, which are known to play an important role in the partitioning of the genome into distinctive compartments and domains. One of the major functions of histone modifications is to recruit reader proteins, which recognize the epigenetic marks and transduce the molecular signals in chromatin to downstream effects. Histone readers are defined protein domains with well-organized three-dimensional structures. In this Chapter, we will outline major histone readers, delineate their biochemical and structural features in histone recognition, and describe how dysregulation of histone readout leads to human cancer.
Collapse
Affiliation(s)
- Hong Wen
- Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA
| | - Xiaobing Shi
- Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI, 49503, USA.
| |
Collapse
|
28
|
Yang Y, Ma X, Xia H, Wang L, Chen S, Xu K, Yang F, Zou Y, Wang Y, Zhu J, Li T, Luo Z, Hu S, Liao Z, Luo L, Yu S. Natural variation of Alfin-like family affects seed size and drought tolerance in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1176-1193. [PMID: 36219491 DOI: 10.1111/tpj.16003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The Alfin-like (AL) family is a group of small plant-specific transcriptional factors involved in abiotic stresses in dicotyledon. In an early study, we found an AL gene in rice that was associated with grain yield under drought stress. However, little information is known about the AL family in rice. In this study, AL genes in the rice genome were identified, and the OsAL proteins were found to locate in the nucleus and have no transcriptional self-activation activity. The expression of the OsALs was regulated by different environmental stimulations and plant hormones. Association and domestication analysis revealed that natural variation of most OsALs was significantly associated with yield traits, drought resistance and divergence in grain size in indica and japonica rice varieties. Hap1 of OsAL7.1 and Hap7 of OsAL11 were favorable haplotypes of seed weight and germination under osmotic stress. Furthermore, osal7.1 and osal11 mutants have larger seeds and are more sensitive to abscisic acid and mannitol during germination stage. Overexpressing of OsAL7.1 and OsAL11 in rice weakened the tolerance to drought in the adult stage. Thus, our work provides informative knowledge for exploring and harnessing haplotype diversity of OsALs to improve yield stability under drought stress.
Collapse
Affiliation(s)
- Yunan Yang
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- The Research Center for Plant Functional Genes and Tissue Culture Technology of Jiangxi Agricultural University, 1101# Zhimin Avenue, Nanchang, Jiangxi, 330045, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Hui Xia
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Lei Wang
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Shoujun Chen
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Kai Xu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Fangwen Yang
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Yuqiao Zou
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Yulan Wang
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Jinmin Zhu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- The Research Center for Plant Functional Genes and Tissue Culture Technology of Jiangxi Agricultural University, 1101# Zhimin Avenue, Nanchang, Jiangxi, 330045, China
| | - Tianfei Li
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Zhi Luo
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Songping Hu
- The Research Center for Plant Functional Genes and Tissue Culture Technology of Jiangxi Agricultural University, 1101# Zhimin Avenue, Nanchang, Jiangxi, 330045, China
| | - Zhigang Liao
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| | - Shunwu Yu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, 2901# Beidi Road, Minhang District, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, 2901# Beidi Road, Minghang District, Shanghai, 201106, China
| |
Collapse
|
29
|
Franco-Echevarría E, Rutherford TJ, Fiedler M, Dean C, Bienz M. Plant vernalization proteins contain unusual PHD superdomains without histone H3 binding activity. J Biol Chem 2022; 298:102540. [PMID: 36174674 PMCID: PMC9640981 DOI: 10.1016/j.jbc.2022.102540] [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: 07/05/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022] Open
Abstract
PHD fingers are modular domains in chromatin-associated proteins that decode the methylation status of histone H3 tails. A PHD finger signature is found in plant vernalization (VEL) proteins, which function as accessory factors of the Polycomb system to control flowering in Arabidopsis through an epigenetic silencing mechanism. It has been proposed that VEL PHD fingers bind to methylated histone H3 tails to facilitate association of the Polycomb silencing machinery with target genes. Here, we use structural analysis by X-ray crystallography to show that the VEL PHD finger forms the central module of a larger compact tripartite superdomain that also contains a zinc finger and a four-helix bundle. This PHD superdomain fold is only found in one other family, the OBERON proteins, which have multiple functions in Arabidopsis meristems to control plant growth. The putative histone-binding surface of OBERON proteins exhibits the characteristic three-pronged pocket of histone-binding PHD fingers and binds to methylated histone H3 tails. However, that of VEL PHD fingers lacks this architecture and exhibits unusually high positive surface charge. This VEL PHD superdomain neither binds to unmodified nor variously modified histone H3 tails, as demonstrated by isothermal calorimetry and NMR spectroscopy. Instead, the VEL PHD superdomain interacts with negatively charged polymers. Our evidence argues for evolution of a divergent function for the PHD superdomain in vernalization that does not involve histone tail decoding.
Collapse
Affiliation(s)
| | | | - Marc Fiedler
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Caroline Dean
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom; John Innes Centre, Norwich Research Park, Norwich, United Kingdom.
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
| |
Collapse
|
30
|
Fraschilla I, Amatullah H, Rahman RU, Jeffrey KL. Immune chromatin reader SP140 regulates microbiota and risk for inflammatory bowel disease. Cell Host Microbe 2022; 30:1370-1381.e5. [PMID: 36130593 PMCID: PMC10266544 DOI: 10.1016/j.chom.2022.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 12/25/2022]
Abstract
Inflammatory bowel disease (IBD) is driven by host genetics and environmental factors, including commensal microorganisms. Speckled Protein 140 (SP140) is an immune-restricted chromatin "reader" that is associated with Crohn's disease (CD), multiple sclerosis (MS), and chronic lymphocytic leukemia (CLL). However, the disease-causing mechanisms of SP140 remain undefined. Here, we identify an immune-intrinsic role for SP140 in regulating phagocytic defense responses to prevent the expansion of inflammatory bacteria. Mice harboring altered microbiota due to hematopoietic Sp140 deficiency exhibited severe colitis that was transmissible upon cohousing and ameliorated with antibiotics. Loss of SP140 results in blooms of Proteobacteria, including Helicobacter in Sp140-/- mice and Enterobacteriaceae in humans bearing the CD-associated SP140 loss-of-function variant. Phagocytes from patients with the SP140 loss-of-function variant and Sp140-/- mice exhibited altered antimicrobial defense programs required for control of pathobionts. Thus, mutations within this epigenetic reader may constitute a predisposing event in human diseases provoked by microbiota.
Collapse
Affiliation(s)
- Isabella Fraschilla
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Raza-Ur Rahman
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kate L Jeffrey
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Massachusetts Institute of Technology Center for Microbiome, Informatics and Therapeutics, Cambridge, MA 02139, USA.
| |
Collapse
|
31
|
Gül N, Yıldız A. An in silico study of how histone tail conformation affects the binding affinity of ING family proteins. PeerJ 2022; 10:e14029. [PMID: 36199288 PMCID: PMC9528904 DOI: 10.7717/peerj.14029] [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: 05/30/2022] [Accepted: 08/16/2022] [Indexed: 01/19/2023] Open
Abstract
Background Due to its intrinsically disordered nature, the histone tail is conformationally heterogenic. Therefore, it provides specific binding sites for different binding proteins or factors through reversible post-translational modifications (PTMs). For instance, experimental studies stated that the ING family binds with the histone tail that has methylation on the lysine in position 4. However, numerous complexes featuring a methylated fourth lysine residue of the histone tail can be found in the UniProt database. So the question arose if other factors like the conformation of the histone tail affect the binding affinity. Methods The crystal structure of the PHD finger domain from the proteins ING1, ING2, ING4, and ING5 are docked to four histone H3 tails with two different conformations using Haddock 2.4 and ClusPro. The best four models for each combination are selected and a two-sample t-test is performed to compare the binding affinities of helical conformations vs. linear conformations using Prodigy. The protein-protein interactions are examined using LigPlot. Results The linear histone conformations in predicted INGs-histone H3 complexes exhibit statistically significant higher binding affinity than their helical counterparts (confidence level of 99%). The outputs of predicted models generated by the molecular docking programs Haddock 2.4 and ClusPro are comparable, and the obtained protein-protein interaction patterns are consistent with experimentally confirmed binding patterns. Conclusion The results show that the conformation of the histone tail is significantly affecting the binding affinity of the docking protein. Herewith, this in silico study demonstrated in detail the binding preference of the ING protein family to histone H3 tail. Further research on the effect of certain PTMs on the final tail conformation and the interaction between those factors seem to be promising for a better understanding of epigenetics.
Collapse
Affiliation(s)
- Nadir Gül
- Faculty of Natural Sciences, Turkish-German University, Istanbul, Turkey
| | - Ahmet Yıldız
- Faculty of Engineering, Turkish-German University, Istanbul, Turkey
| |
Collapse
|
32
|
Szarka-Kovács AB, Takács Z, Bence M, Erdélyi M, Jankovics F. Drosophila MESR4 Gene Ensures Germline Stem Cell Differentiation by Promoting the Transcription of bag of marbles. Cells 2022; 11:cells11132056. [PMID: 35805140 PMCID: PMC9265997 DOI: 10.3390/cells11132056] [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: 05/30/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Ovarian germline stem cells (GSCs) of Drosophila melanogaster provide a valuable in vivo model to investigate how the adult stem cell identity is maintained and the differentiation of the daughter cells is regulated. GSCs are embedded into a specialized cellular microenvironment, the so-called stem cell niche. Besides the complex signaling interactions between the germ cells and the niche cells, the germ cell intrinsic mechanisms, such as chromatin regulation and transcriptional control, are also crucial in the decision about self-renewal and differentiation. The key differentiation regulator gene is the bag of marbles (bam), which is transcriptionally repressed in the GSCs and de-repressed in the differentiating daughter cell. Here, we show that the transcription factor MESR4 functions in the germline to promote GSC daughter differentiation. We find that the loss of MESR4 results in the accumulation of GSC daughter cells which fail to transit from the pre-cystoblast (pre-CB) to the differentiated cystoblast (CB) stage. The forced expression of bam can rescue this differentiation defect. By a series of epistasis experiments and a transcriptional analysis, we demonstrate that MESR4 positively regulates the transcription of bam. Our results suggest that lack of repression alone is not sufficient, but MESR4-mediated transcriptional activation is also required for bam expression.
Collapse
Affiliation(s)
- Alexandra Brigitta Szarka-Kovács
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary; (A.B.S.-K.); (Z.T.); (M.B.)
- Doctoral School in Biology, University of Szeged, H-6720 Szeged, Hungary
| | - Zsanett Takács
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary; (A.B.S.-K.); (Z.T.); (M.B.)
| | - Melinda Bence
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary; (A.B.S.-K.); (Z.T.); (M.B.)
| | - Miklós Erdélyi
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary; (A.B.S.-K.); (Z.T.); (M.B.)
- Correspondence: (M.E.); (F.J.)
| | - Ferenc Jankovics
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary; (A.B.S.-K.); (Z.T.); (M.B.)
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Correspondence: (M.E.); (F.J.)
| |
Collapse
|
33
|
Lv Y, Lin W. Comprehensive analysis of the expression, prognosis, and immune infiltrates for CHDs in human lung cancer. Discov Oncol 2022; 13:29. [PMID: 35467222 PMCID: PMC9038980 DOI: 10.1007/s12672-022-00489-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/19/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The chromodomain helicase DNA-binding (CHD) family, a group of genes that regulate nucleosome spacing and access to transcription factors, contributes to tumorigenesis in various cancers. However, the roles of CHD family members in lung cancer remain poorly understood. METHODS We investigated the transcriptional, survival, and immune data of CHDs in patients with lung cancer from the Oncomine, UALCAN, GEPIA, Kaplan-Meier Plotter, TCGA, TIMER, cBioPortal, and CR2Cancer databases. Then, perform functional enrichment analysis of CHDs was performed using the Metascape. Finally, the expression of CHD7, CHD8 and DNA damage response genes were evaluated by quantitative real-time PCR and western blot.The effects of CHD7 or CHD8 knockdown on A549 and PC9 cells were measured in vitro by flow cytometry, cell viability and colony formation assays. RESULTS We found that except for CHD5, nearly all members of CHDs in lung cancer showed altered expression compared with adjacent normal tissues. Moreover, the abnormal expression levels of CHDs were related to the clinical outcome of patients with lung adenocarcinoma and, to a lesser extent, patients with lung squamous cell carcinoma, which were significantly associated with the immune infiltrating levels of immune cells. Furthermore, the functions of CHDs and their neighboring genes are mainly related to DNA repair, the cell cycle, and organelle organization. Finally, cellular experiments conducted in vitro confirmed that CHD7/8 played indispensable roles in DNA damage signaling and cell cycle progression in lung adenocarcinoma cells. CONCLUSION This study implied that CHD family members, especially in subclass III, are potential targets of precision therapy and new biomarkers for patients with lung cancer.
Collapse
Affiliation(s)
- Yang Lv
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China
- University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Wenchu Lin
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China.
| |
Collapse
|
34
|
Guk JY, Jang MJ, Kim S. Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses. BMC PLANT BIOLOGY 2022; 22:206. [PMID: 35443608 PMCID: PMC9020097 DOI: 10.1186/s12870-022-03580-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/06/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays an important role in epigenetics by regulating gene expression in eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies. RESULTS We performed genome-wide re-annotation in Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice), Capsicum annuum (pepper), Solanum tuberosum (potato), and Solanum lycopersicum (tomato) to better understand the role of PHD-finger genes in these species. Our investigation identified 875 PHD-finger genes, of which 225 (26% of total) were newly identified, including 57 (54%) novel PHD-finger genes in pepper. The PHD-finger genes of the five plant species have various integrated domains that may be responsible for the diversification of structures and functions of these genes. Evolutionary analyses suggest that PHD-finger genes were expanded recently by lineage-specific duplication, especially in pepper and potato, resulting in diverse repertoires of PHD-finger genes among the species. We validated the expression of six newly identified PHD-finger genes in pepper with qRT-PCR. Transcriptome analyses suggest potential functions of PHD-finger genes in response to various abiotic stresses in pepper. CONCLUSIONS Our data, including the updated annotation of PHD-finger genes, provide useful information for further evolutionary and functional analyses to better understand the roles of the PHD-finger gene family in pepper.
Collapse
Affiliation(s)
- Ji-Yoon Guk
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Min-Jeong Jang
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea.
| |
Collapse
|
35
|
Kim JH, Lee JE, Jang CS. Regulation of Oryza sativa molybdate transporter1;3 degradation via RING finger E3 ligase OsAIR3. JOURNAL OF PLANT PHYSIOLOGY 2021; 264:153484. [PMID: 34343729 DOI: 10.1016/j.jplph.2021.153484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/19/2021] [Accepted: 07/25/2021] [Indexed: 05/29/2023]
Abstract
High concentrations of As in contaminated environments pose a serious threat to plant, human, and animal health. In this study, we characterized an As-responsive Really Interesting New Gene (RING) E3 ubiquitin ligase gene under arsenate (AsV) stress, named as Oryza sativa As-Induced RING E3 ligase 3 (OsAIR3). AsV treatment highly induced the expression of OsAIR3. OsAIR3-EYFP was localized to the nucleus in rice protoplasts and exhibited E3 ligase activity. Yeast two-hybrid screening and bimolecular fluorescence complementation and pull-down assays revealed the interaction of OsAIR3 with an O. sativa molybdate transporter (OsMOT1;3) in the plasma membrane and cytoplasm. In addition, an in vitro cell-free degradation assay was performed to demonstrate the degradation of OsMOT1;3 by OsAIR3 via the 26S proteasome system. Heterogeneous overexpression of OsAIR3 in Arabidopsis yielded AsV-tolerant phenotypes, as indicated by the comparison of cotyledon expansion, root elongation, shoot fresh weight, and As accumulation between the OsAIR3-overexpressing and control plants. Collectively, these findings suggest that OsAIR3 positively regulates plant response to AsV stress.
Collapse
Affiliation(s)
- Ju Hee Kim
- Plant Genomics Laboratory, Department of Bio-resources Sciences, Graduate School, Kangwon National University, Chuncheon, 24341, South Korea
| | - Jeong Eun Lee
- Plant Genomics Laboratory, Department of Bio-resources Sciences, Graduate School, Kangwon National University, Chuncheon, 24341, South Korea
| | - Cheol Seong Jang
- Plant Genomics Laboratory, Department of Bio-resources Sciences, Graduate School, Kangwon National University, Chuncheon, 24341, South Korea; Interdisciplinary Program in Smart Agriculture, Graduate School, Kangwon National University, Chuncheon, 24341, South Korea.
| |
Collapse
|
36
|
Blasl AT, Schulze S, Qin C, Graf LG, Vogt R, Lammers M. Post-translational lysine ac(et)ylation in health, ageing and disease. Biol Chem 2021; 403:151-194. [PMID: 34433238 DOI: 10.1515/hsz-2021-0139] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]
Abstract
The acetylation/acylation (ac(et)ylation) of lysine side chains is a dynamic post-translational modification (PTM) regulating fundamental cellular processes with implications on the organisms' ageing process: metabolism, transcription, translation, cell proliferation, regulation of the cytoskeleton and DNA damage repair. First identified to occur on histones, later studies revealed the presence of lysine ac(et)ylation in organisms of all kingdoms of life, in proteins covering all essential cellular processes. A remarkable finding showed that the NAD+-dependent sirtuin deacetylase Sir2 has an impact on replicative lifespan in Saccharomyces cerevisiae suggesting that lysine acetylation has a direct role in the ageing process. Later studies identified sirtuins as mediators for beneficial effects of caloric/dietary restriction on the organisms' health- or lifespan. However, the molecular mechanisms underlying these effects are only incompletely understood. Progress in mass-spectrometry, structural biology, synthetic and semi-synthetic biology deepened our understanding of this PTM. This review summarizes recent developments in the research field. It shows how lysine ac(et)ylation regulates protein function, how it is regulated enzymatically and non-enzymatically, how a dysfunction in this post-translational machinery contributes to disease development. A focus is set on sirtuins and lysine acyltransferases as these are direct sensors and mediators of the cellular metabolic state. Finally, this review highlights technological advances to study lysine ac(et)ylation.
Collapse
Affiliation(s)
- Anna-Theresa Blasl
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Sabrina Schulze
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Chuan Qin
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Leonie G Graf
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Robert Vogt
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Michael Lammers
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| |
Collapse
|
37
|
Si S, Zhang M, Hu Y, Wu C, Yang Y, Luo S, Xiao X. BrcuHAC1 is a histone acetyltransferase that affects bolting development in Chinese flowering cabbage. J Genet 2021. [DOI: 10.1007/s12041-021-01303-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
38
|
Begum NA, Haque F, Stanlie A, Husain A, Mondal S, Nakata M, Taniguchi T, Taniguchi H, Honjo T. Phf5a regulates DNA repair in class switch recombination via p400 and histone H2A variant deposition. EMBO J 2021; 40:e106393. [PMID: 33938017 PMCID: PMC8204862 DOI: 10.15252/embj.2020106393] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Antibody class switch recombination (CSR) is a locus-specific genomic rearrangement mediated by switch (S) region transcription, activation-induced cytidine deaminase (AID)-induced DNA breaks, and their resolution by non-homologous end joining (NHEJ)-mediated DNA repair. Due to the complex nature of the recombination process, numerous cofactors are intimately involved, making it important to identify rate-limiting factors that impact on DNA breaking and/or repair. Using an siRNA-based loss-of-function screen of genes predicted to encode PHD zinc-finger-motif proteins, we identify the splicing factor Phf5a/Sf3b14b as a novel modulator of the DNA repair step of CSR. Loss of Phf5a severely impairs AID-induced recombination, but does not perturb DNA breaks and somatic hypermutation. Phf5a regulates NHEJ-dependent DNA repair by preserving chromatin integrity to elicit optimal DNA damage response and subsequent recruitment of NHEJ factors at the S region. Phf5a stabilizes the p400 histone chaperone complex at the locus, which in turn promotes deposition of H2A variant such as H2AX and H2A.Z that are critical for the early DNA damage response and NHEJ, respectively. Depletion of Phf5a or p400 blocks the repair of both AID- and I-SceI-induced DNA double-strand breaks, supporting an important contribution of this axis to programmed as well as aberrant recombination.
Collapse
Affiliation(s)
- Nasim A Begum
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Farazul Haque
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Andre Stanlie
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- BioMedicine DesignPfizer Inc.CambridgeMAUSA
| | - Afzal Husain
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- Department of BiochemistryFaculty of Life SciencesAligarh Muslim UniversityAligarhIndia
| | - Samiran Mondal
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- Department of ChemistryRammohan CollegeKolkataIndia
| | - Mikiyo Nakata
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Takako Taniguchi
- Division of Disease ProteomicsInstitute for Enzyme ResearchUniversity of TokushimaTokushimaJapan
| | - Hisaaki Taniguchi
- Division of Disease ProteomicsInstitute for Enzyme ResearchUniversity of TokushimaTokushimaJapan
| | - Tasuku Honjo
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| |
Collapse
|
39
|
Park IG, Jeon M, Kim H, Lee JM. Coordinated methyl readers: Functional communications in cancer. Semin Cancer Biol 2021; 83:88-99. [PMID: 33753223 DOI: 10.1016/j.semcancer.2021.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/18/2021] [Accepted: 03/16/2021] [Indexed: 01/28/2023]
Abstract
Methylation is a major post-translational modification (PTM) generated by methyltransferase on target proteins; it is recognized by the epigenetic reader to expand the functional diversity of proteins. Methylation can occur on specific lysine or arginine residues localized within regulatory domains in both histone and nonhistone proteins, thereby allowing distinguished properties of the targeted protein. Methylated residues are recognized by chromodomain, malignant brain tumor (MBT), Tudor, plant homeodomain (PHD), PWWP, WD-40, ADD, and ankyrin repeats by an induced-fit mechanism. Methylation-dependent activities regulate distinct aspects of target protein function and are largely reliant on methyl readers of histone and nonhistone proteins in various diseases. Methylation of nonhistone proteins that are recognized by methyl readers facilitates the degradation of unwanted proteins, as well as the stabilization of necessary proteins. Unlike nonhistone substrates, which are mainly monomethylated by methyltransferase, histones are di- or trimethylated by the same methyltransferases and then connected to other critical regulators by methyl readers. These fine-tuned controls by methyl readers are significant for the progression or inhibition of diseases, including cancers. Here, current knowledge and our perspectives about regulating protein function by methyl readers are summarized. We also propose that expanded research on the strong crosstalk mechanisms between methylation and other PTMs via methyl readers would augment therapeutic research in cancer.
Collapse
Affiliation(s)
- Il-Geun Park
- Department of Molecular Bioscience, College of Biomedical Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Minsol Jeon
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Hyunkyung Kim
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea.
| | - Ji Min Lee
- Department of Molecular Bioscience, College of Biomedical Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
| |
Collapse
|
40
|
Wu H, Zheng L, Qanmber G, Guo M, Wang Z, Yang Z. Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.). BMC PLANT BIOLOGY 2021; 21:13. [PMID: 33407131 PMCID: PMC7788912 DOI: 10.1186/s12870-020-02787-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/08/2020] [Indexed: 05/07/2023]
Abstract
BACKGROUND The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton. RESULTS In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome. However, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions. CONCLUSION This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.
Collapse
Affiliation(s)
- Huanhuan Wu
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Lei Zheng
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Mengzhen Guo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| |
Collapse
|
41
|
Waziri A, Singh DK, Sharma T, Chatterjee S, Purty RS. Genome-wide analysis of PHD finger gene family and identification of potential miRNA and their PHD finger gene specific targets in Oryza sativa indica. Noncoding RNA Res 2020; 5:191-200. [PMID: 33163736 PMCID: PMC7610035 DOI: 10.1016/j.ncrna.2020.10.002] [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: 10/06/2020] [Revised: 10/24/2020] [Accepted: 10/24/2020] [Indexed: 11/24/2022] Open
Abstract
Rice (Oryza sativa L.) is one of the most important cereal crops for one third of the world population. However, the grain quality as well as yield of rice is severely affected by various abiotic stresses. Environmental stresses affect the expression of various microRNAs (miRNAs) which in turn negatively regulate gene expression at the post-transcriptional level either by degrading the target mRNA genes or suppressing translation in plants. Plant homeo-domain (PHD) finger proteins are known to be involved in the plant response to salinity stress. In the present study, we identified 44 putative OsPHD finger genes in Oryza sativa Indica, using Ensembl Plants Database. Using computational approach, potential miRNAs that target OsPHD finger genes were identified. Out of the 44 OsPHD finger genes only three OsPHD finger genes i.e., OsPHD2, OsPHD35 and OsPHD11, were found to be targeted by five newly identified putative miRNAs i.e., ath-miRf10010-akr, ath-miRf10110-akr, osa-miR1857–3p, osa-miRf10863-akr, and osa-miRf11806-akr. This is the first report of these five identified miRNAs on targeting PHD finger in Oryza sativa Indica. Further, expression analysis of 44 PHD finger genes under salinity was also performed using quantitative Real-Time PCR. The expression profile of 8 genes were found to be differentially regulated, among them two genes were significantly up regulated i.e., OsPHD6 and OsPHD12. In silico protein-protein interaction analysis using STRING database showed interaction of the OsPHD finger proteins with other protein partners that are directly or indirectly involved in development and abiotic stress tolerance. Total of 44 Plant homeo-domain (PHD) finger proteins were identified & classified into 10 groups in Oryza sativa Indica. This is the first report showing 5 newly identified putative miRNAs targeting three OsPHD genes i.e., OsPHD2, 11 and 35. Expression analysis of PHD finger genes showed up-regulation of the 2 genes OsPHD 6 & 12 under salinity stress treatment. Protein-protein network of OsPHDs showed protein partners that are involved in plant growth and abiotic stress tolerance.
Collapse
Affiliation(s)
- Aafrin Waziri
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Deepak Kumar Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Tarun Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Sayan Chatterjee
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Ram Singh Purty
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| |
Collapse
|
42
|
Zhang L, Lu Y, Wang Y, Wang F, Zhai S, Chen Z, Cai Z. PHF14 is required for germinal center B cell development. Cell Immunol 2020; 358:104221. [PMID: 33035772 DOI: 10.1016/j.cellimm.2020.104221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/03/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
Germinal centers (GCs), which are the site of antibody diversification and affinity maturation, are vitally important for humoral immunity. GC B cell proliferation is essentially for these processes by providing enough templates for somatic hypermutation (SHM) and serving as a critical mechanism of positive selection. In the current study, we found a significant reduction of GC response in the spleens of GC B cell specific PHF14 knockout (PHF14GCB KO) mice compared with the wild-type control (PHF14GCB WT) when the mice were challenged with SRBCs or lymphocytic choriomeningitis virus. We also demonstrated that PHF14 did not affect the cell survival of GC B cells, but regulated the proliferation of GC B cells. In addition, PHF14 suppressed the expression of Cdkn1a (p21) though regulating the level of H3K4me3 to control the proliferation of GC B cells. Collectively, our data suggest that PHF14 plays an important role in the process of germinal center formation by regulating GC B cell proliferation in spleen.
Collapse
Affiliation(s)
- Le Zhang
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjin 211166, China; Analysis Center, Nanjing Medical University, Nanjing 211166, China
| | - Yanlai Lu
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjin 211166, China
| | - Yuliang Wang
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjin 211166, China
| | - Feng Wang
- Analysis Center, Nanjing Medical University, Nanjing 211166, China
| | - Sulan Zhai
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjin 211166, China
| | - Zhengjun Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yueyang Road, 200031 Shanghai, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 200031, China
| | - Zhenming Cai
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjin 211166, China.
| |
Collapse
|
43
|
Zhou S, Feng S, Qin W, Wang X, Tang Y, Yuan S. Epigenetic Regulation of Spermatogonial Stem Cell Homeostasis: From DNA Methylation to Histone Modification. Stem Cell Rev Rep 2020; 17:562-580. [PMID: 32939648 DOI: 10.1007/s12015-020-10044-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 12/27/2022]
Abstract
Spermatogonial stem cells(SSCs)are the ultimate germline stem cells with the potential of self-renewal and differentiation, and a dynamic balance of SSCs play an essential role in spermatogenesis. During the gene expression process, genomic DNA and nuclear protein, working together, contribute to SSC homeostasis. Recently, emerging studies have shown that epigenome-related molecules such as chromatin modifiers play an important role in SSC homeostasis through regulating target gene expression. Here, we focus on two types of epigenetic events, including DNA methylation and histone modification, and summarize their function in SSC homeostasis. Understanding the molecular mechanism during SSC homeostasis will promote the recognition of epigenetic biomarkers in male infertility, and bring light into therapies of infertile patients.Graphical Abstract.
Collapse
Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Shenglei Feng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, 510500, Guangzhou, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Yunge Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, 510500, Guangzhou, China.
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China. .,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, 518057, China.
| |
Collapse
|
44
|
Structure and function of Pygo in organ development dependent and independent Wnt signalling. Biochem Soc Trans 2020; 48:1781-1794. [PMID: 32677664 DOI: 10.1042/bst20200393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 11/17/2022]
Abstract
Pygo is a nuclear protein containing two conserved domains, NHD and PHD, which play important roles in embryonic development and carcinogenesis. Pygo was first identified as a core component of the Wnt/β-catenin signalling pathway. However, it has also been reported that the function of Pygo is not always Wnt/β-catenin signalling dependent. In this review, we summarise the functions of both domains of Pygo and show that their functions are synergetic. The PHD domain mainly combines with transcription co-factors, including histone 3 and Bcl9/9l. The NHD domain mainly recruits histone methyltransferase/acetyltransferase (HMT/HAT) to modify lysine 4 of the histone 3 tail (H3K4) and interacts with Chip/LIM-domain DNA-binding proteins (ChiLS) to form enhanceosomes to regulate transcriptional activity. Furthermore, we summarised chromatin modification differences of Pygo in Drosophila (dPygo) and vertebrates, and found that Pygo displayes a chromatin silencing function in Drosophila, while in vertebates, Pygo has a chromatin-activating function due to the two substitution of two amino acid residues. Next, we confirmed the relationship between Pygo and Bcl9/9l and found that Pygo-Bcl/9l are specifically partnered both in the nucleus and in the cytoplasm. Finally, we discuss whether transcriptional activity of Pygo is Wnt/β-catenin dependent during embryonic development. Available information indications that the transcriptional activity of Pygo in embryonic development is either Wnt/β-catenin dependent or independent in both tissue-specific and cell-specific-modes.
Collapse
|
45
|
Chen R, Zhang M, Zhou Y, Guo W, Yi M, Zhang Z, Ding Y, Wang Y. The application of histone deacetylases inhibitors in glioblastoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:138. [PMID: 32682428 PMCID: PMC7368699 DOI: 10.1186/s13046-020-01643-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022]
Abstract
The epigenetic abnormality is generally accepted as the key to cancer initiation. Epigenetics that ensure the somatic inheritance of differentiated state is defined as a crucial factor influencing malignant phenotype without altering genotype. Histone modification is one such alteration playing an essential role in tumor formation, progression, and resistance to treatment. Notably, changes in histone acetylation have been strongly linked to gene expression, cell cycle, and carcinogenesis. The balance of two types of enzyme, histone acetyltransferases (HATs) and histone deacetylases (HDACs), determines the stage of histone acetylation and then the architecture of chromatin. Changes in chromatin structure result in transcriptional dysregulation of genes that are involved in cell-cycle progression, differentiation, apoptosis, and so on. Recently, HDAC inhibitors (HDACis) are identified as novel agents to keep this balance, leading to numerous researches on it for more effective strategies against cancers, including glioblastoma (GBM). This review elaborated influences on gene expression and tumorigenesis by acetylation and the antitumor mechanism of HDACis. Besdes, we outlined the preclinical and clinical advancement of HDACis in GBM as monotherapies and combination therapies.
Collapse
Affiliation(s)
- Rui Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Mengxian Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Yangmei Zhou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenjing Guo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ming Yi
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ziyan Zhang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510000, Guangdong, China
| | - Yanpeng Ding
- Department of Oncology, Zhongnan Hospital, Wuhan University, Wuhan, 430030, China
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| |
Collapse
|
46
|
Kane M, Mele V, Liberatore RA, Bieniasz PD. Inhibition of spumavirus gene expression by PHF11. PLoS Pathog 2020; 16:e1008644. [PMID: 32678836 PMCID: PMC7390438 DOI: 10.1371/journal.ppat.1008644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/29/2020] [Accepted: 05/19/2020] [Indexed: 01/05/2023] Open
Abstract
The foamy viruses (FV) or spumaviruses are an ancient subfamily of retroviruses that infect a variety of vertebrates. FVs are endemic, but apparently apathogenic, in modern non-human primates. Like other retroviruses, FV replication is inhibited by type-I interferon (IFN). In a previously described screen of IFN-stimulated genes (ISGs), we identified the macaque PHD finger domain protein-11 (PHF11) as an inhibitor of prototype foamy virus (PFV) replication. Here, we show that human and macaque PHF11 inhibit the replication of multiple spumaviruses, but are inactive against several orthoretroviruses. Analysis of other mammalian PHF11 proteins revealed that antiviral activity is host species dependent. Using multiple reporter viruses and cell lines, we determined that PHF11 specifically inhibits a step in the replication cycle that is unique to FVs, namely basal transcription from the FV internal promoter (IP). In so doing, PHF11 prevents expression of the viral transactivator Tas and subsequent activation of the viral LTR promoter. These studies reveal a previously unreported inhibitory mechanism in mammalian cells, that targets a family of ancient viruses and may promote viral latency.
Collapse
Affiliation(s)
- Melissa Kane
- Department of Pediatrics, Infectious Diseases Division, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Microbial Pathogenesis, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Vincent Mele
- Department of Pediatrics, Infectious Diseases Division, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Microbial Pathogenesis, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Rachel A. Liberatore
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
| |
Collapse
|
47
|
Transcriptome Analysis of High-NUE (T29) and Low-NUE (T13) Genotypes Identified Different Responsive Patterns Involved in Nitrogen Stress in Ramie ( Boehmeria nivea (L.) Gaudich). PLANTS 2020; 9:plants9060767. [PMID: 32575463 PMCID: PMC7356044 DOI: 10.3390/plants9060767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/22/2022]
Abstract
Nitrogen-use efficiency (NUE) has significant impacts on plant growth and development. NUE in plants differs substantially in physiological resilience to nitrogen stress; however, the molecular mechanisms underlying enhanced resilience of high-NUE plants to nitrogen deficiency remains unclear. We compared transcriptome-wide gene expression between high-NUE and low-NUE ramie (Boehmeria nivea (L.) Gaudich) genotypes under nitrogen (N)-deficient and normal conditions to identify the transcriptomic expression patterns that contribute to ramie resilience to nitrogen deficiency. Two ramie genotypes with contrasting NUE were used in the study, including T29 (NUE = 46.01%) and T13 (NUE = 15.81%). Our results showed that high-NUE genotypes had higher gene expression under the control condition across 94 genes, including frontloaded genes such as GDSL esterase and lipase, gibberellin, UDP-glycosyltransferase, and omega-6 fatty acid desaturase. Seventeen stress-tolerance genes showed lower expression levels and varied little in response to N-deficiency stress in high-NUE genotypes. In contrast, 170 genes were upregulated under N deficiency in high-NUE genotypes but downregulated in low-NUE genotypes compared with the controls. Furthermore, we identified the potential key genes that enable ramie to maintain physiological resilience under N-deficiency stress, and categorized these genes into three groups based on the transcriptome and their expression patterns. The transcriptomic and clustering analysis of these nitrogen-utilization-related genes could provide insight to better understand the mechanism of linking among the three gene classes that enhance resilience in high-NUE ramie genotypes.
Collapse
|
48
|
PHF14 Promotes Cell Proliferation and Migration through the AKT and ERK1/2 Pathways in Gastric Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6507510. [PMID: 32596345 PMCID: PMC7305535 DOI: 10.1155/2020/6507510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
PHF14 is a new member belonging to PHD finger proteins. PHF14 is involved in multiple biologic processes including Dandy–Walker syndrome, mesenchyme growth, lung fibrosis, renal fibrosis, persistent pulmonary hypertension, and tumor development. This study aims to explore whether PHF14 plays an important role in gastric cancer. Here, PHF14 is indicated as a tumor promoter. The expression of PHF14 enhances no matter in clinical samples or in gastric cancer cells. High expression of PHF14 impairs survival of patients. Attenuation of PHF14 inhibits cell proliferation in gastric cancer cells. PHF14 downregulation inhibits the expression of cell cycle-related proteins, CDK6 and cyclin D1. Furthermore, silencing of PHF14 reduces the level of phosphorylated AKT as well as phosphorylated ERK1/2. Finally, downregulation of PHF14 in gastric cancer cells inhibits colony formation in vitro and tumorigenesis in vivo. These results indicate that PHF14 promotes tumor development in gastric cancer, so PHF14 thereby acts as a potential target for gastric cancer therapy.
Collapse
|
49
|
Abdelfettah S, Boulay G, Dubuissez M, Spruyt N, Garcia SP, Rengarajan S, Loison I, Leroy X, Rivera MN, Leprince D. hPCL3S promotes proliferation and migration of androgen-independent prostate cancer cells. Oncotarget 2020; 11:1051-1074. [PMID: 32256978 PMCID: PMC7105160 DOI: 10.18632/oncotarget.27511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) allows the deposition of H3K27me3. PRC2 facultative subunits modulate its activity and recruitment such as hPCL3/PHF19, a human ortholog of Drosophila Polycomb-like protein (PCL). These proteins contain a TUDOR domain binding H3K36me3, two PHD domains and a “Winged-helix” domain involved in GC-rich DNA binding. The human PCL3 locus encodes the full-length hPCL3L protein and a shorter isoform, hPCL3S containing the TUDOR and PHD1 domains only. In this study, we demonstrated by RT-qPCR analyses of 25 prostate tumors that hPCL3S is frequently up-regulated. In addition, hPCL3S is overexpressed in the androgen-independent DU145 and PC3 cells, but not in the androgen-dependent LNCaP cells. hPCL3S knockdown decreased the proliferation and migration of DU145 and PC3 whereas its forced expression into LNCaP increased these properties. A mutant hPCL3S unable to bind H3K36me3 (TUDOR-W50A) increased proliferation and migration of LNCaP similarly to wt hPCL3S whereas inactivation of its PHD1 domain decreased proliferation. These effects partially relied on the up-regulation of genes known to be important for the proliferation and/or migration of prostate cancer cells such as S100A16, PlexinA2, and Spondin1. Collectively, our results suggest hPCL3S as a new potential therapeutic target in castration resistant prostate cancers.
Collapse
Affiliation(s)
- Souhila Abdelfettah
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Gaylor Boulay
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Marion Dubuissez
- Present Address: Maisonneuve-Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC H1T 3W5, Canada
| | - Nathalie Spruyt
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Sara P Garcia
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Shruthi Rengarajan
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ingrid Loison
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| | - Xavier Leroy
- Department of Pathology, University de Lille, CHU de Lille, F-59000 Lille, France
| | - Miguel N Rivera
- Department of Pathology, Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Dominique Leprince
- University de Lille, CNRS, Institut Pasteur de Lille, UMR 8161m M3T, Mechanisms of Tumorigenesis and Targeted Therapies, F-59000 Lille, France
| |
Collapse
|
50
|
Karia D, Gilbert RCG, Biasutto AJ, Porcher C, Mancini EJ. The histone H3K4 demethylase JARID1A directly interacts with haematopoietic transcription factor GATA1 in erythroid cells through its second PHD domain. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191048. [PMID: 32218938 PMCID: PMC7029945 DOI: 10.1098/rsos.191048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Chromatin remodelling and transcription factors play important roles in lineage commitment and development through control of gene expression. Activation of selected lineage-specific genes and repression of alternative lineage-affiliated genes result in tightly regulated cell differentiation transcriptional programmes. However, the complex functional and physical interplay between transcription factors and chromatin-modifying enzymes remains elusive. Recent evidence has implicated histone demethylases in normal haematopoietic differentiation as well as in malignant haematopoiesis. Here, we report an interaction between H3K4 demethylase JARID1A and the haematopoietic-specific master transcription proteins SCL and GATA1 in red blood cells. Specifically, we observe a direct physical contact between GATA1 and the second PHD domain of JARID1A. This interaction has potential implications for normal and malignant haematopoiesis.
Collapse
Affiliation(s)
- Dimple Karia
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Robert C. G. Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Antonio J. Biasutto
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Department of Biochemistry, University of Oxford, 3 S Parks Road, Oxford OX1 3QU, UK
| | - Catherine Porcher
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Erika J. Mancini
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RH, UK
| |
Collapse
|