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Rehman M, Agarwal V, Chaudhary R, Kaushik AS, Srivastava S, Srivastava S, Kumar A, Singh S, Mishra V. Pharmacological inhibition of histone deacetylase alleviates chronic unpredictable stress induced atherosclerosis and endothelial dysfunction via upregulation of BDNF. Biochem Biophys Res Commun 2024; 735:150485. [PMID: 39098273 DOI: 10.1016/j.bbrc.2024.150485] [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: 06/02/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
Long-term stress is a significant risk factor for cardiovascular diseases, including atherosclerosis and endothelial dysfunction. Moreover, prolonged stress has shown to negatively regulate central BDNF expression. The role of central BDNF in CNS disorders is well studied until recently the peripheral BDNF was also found to be involved in endothelial function regulation and atherosclerosis. The peripheral BDNF and its role in chronic stress-induced atherosclerosis and endothelial dysfunction remain unclear. Therefore, we aimed to elucidate the role of BDNF and its modulation by the HDAC inhibitor valproic acid (VA) in chronic unpredictable stress (CUS)-induced atherosclerosis and endothelial dysfunction. We demonstrated that a 10-week CUS mouse model substantially decreases central and peripheral BDNF expression, resulting in enhanced serum lipid indices, plaque deposition, fibrosis, and CD68 expression in thoracic aortas. Further, parameters associated with endothelial dysfunction such as increased levels of endothelin-1 (ET-1), adhesion molecules like VCAM-1, M1 macrophage markers, and decreased M2 macrophage markers, eNOS expression, and nitrite levels in aortas, were also observed. VA (50 mg/kg, 14 days, i. p.) was administered to mice following 8 weeks of CUS exposure until the end of the experimental procedure. VA significantly prevented the decrease in BDNF, eNOS and nitrite levels, reduced lesion formation and fibrosis in thoracic aortas and increased ET-1, and VCAM-1 followed by M2 polarization in VA-treated mice. The study highlights the potential of epigenetic modulation of BDNF as a therapeutic target, in stress-induced cardiovascular pathologies and suggests that VA could be a promising agent for mitigating CUS-induced endothelial dysfunction and atherosclerosis by BDNF modulation.
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Affiliation(s)
- Mujeeba Rehman
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Vipul Agarwal
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Rishabh Chaudhary
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Arjun Singh Kaushik
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Siddhi Srivastava
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Sukriti Srivastava
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Anand Kumar
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Sanjay Singh
- Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India.
| | - Vikas Mishra
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India.
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Larkin A, Kunze C, Seman M, Levashkevich A, Curran J, Morris-Evans D, Lemieux S, Khalil AS, Ragunathan K. Mapping the dynamics of epigenetic adaptation in S. pombe during heterochromatin misregulation. Dev Cell 2024:S1534-5807(24)00444-1. [PMID: 39094565 DOI: 10.1016/j.devcel.2024.07.006] [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: 07/21/2023] [Revised: 04/04/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Epigenetic mechanisms enable cells to develop novel adaptive phenotypes without altering their genetic blueprint. Recent studies show histone modifications, such as heterochromatin-defining H3K9 methylation (H3K9me), can be redistributed to establish adaptive phenotypes. We developed a precision-engineered genetic approach to trigger heterochromatin misregulation on-demand in fission yeast. This enabled us to trace genome-scale RNA and H3K9me changes over time in long-term, continuous cultures. Adaptive H3K9me establishes over remarkably slow timescales relative to the initiating stress. We captured dynamic H3K9me redistribution events which depend on an RNA binding complex MTREC, ultimately leading to cells converging on an optimal adaptive solution. Upon stress removal, cells relax to new transcriptional and chromatin states, establishing memory that is tunable and primed for future adaptive epigenetic responses. Collectively, we identify the slow kinetics of epigenetic adaptation that allow cells to discover and heritably encode novel adaptive solutions, with implications for drug resistance and response to infection.
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Affiliation(s)
- Ajay Larkin
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Colin Kunze
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Melissa Seman
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | - Justin Curran
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | - Sophia Lemieux
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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3
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Larkin A, Kunze C, Seman M, Levashkevich A, Curran J, Morris-Evans D, Lemieux S, Khalil AS, Ragunathan K. Mapping the dynamics of epigenetic adaptation during heterochromatin misregulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.10.548368. [PMID: 37503217 PMCID: PMC10369875 DOI: 10.1101/2023.07.10.548368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
A classical and well-established mechanism that enables cells to adapt to new and adverse conditions is the acquisition of beneficial genetic mutations. Much less is known about epigenetic mechanisms that allow cells to develop novel and adaptive phenotypes without altering their genetic blueprint. It has been recently proposed that histone modifications, such as heterochromatin-defining H3K9 methylation (H3K9me), normally reserved to maintain genome integrity, can be redistributed across the genome to establish new and potentially adaptive phenotypes. To uncover the dynamics of this process, we developed a precision engineered genetic approach to trigger H3K9me redistribution on-demand in fission yeast. This enabled us to trace genome-scale RNA and chromatin changes over time prior to and during adaptation in long-term continuous cultures. Establishing adaptive H3K9me occurs over remarkably slow time-scales relative to the initiating stress. During this time, we captured dynamic H3K9me redistribution events ultimately leading to cells converging on an optimal adaptive solution. Upon removal of stress, cells relax to new transcriptional and chromatin states rather than revert to their initial (ground) state, establishing a tunable memory for a future adaptive epigenetic response. Collectively, our tools uncover the slow kinetics of epigenetic adaptation that allow cells to search for and heritably encode adaptive solutions, with implications for drug resistance and response to infection.
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4
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Arimbasseri AG, Shukla A, Pradhan AK, Bhargava P. Increased histone acetylation is the signature of repressed state on the genes transcribed by RNA polymerase III. Gene 2024; 893:147958. [PMID: 37923095 DOI: 10.1016/j.gene.2023.147958] [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: 08/10/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Several covalent modifications are found associated with the transcriptionally active chromatin regions constituted by the genes transcribed by RNA polymerase (pol) II. Pol III-transcribed genes code for the small, stable RNA species, which participate in many cellular processes, essential for survival. Pol III transcription is repressed under most of the stress conditions by its negative regulator Maf1. We found that most of the histone acetylations increase with starvation-induced repression on several genes transcribed by the yeast pol III. On one of these genes, SNR6 (coding for the U6snRNA), a strongly positioned nucleosome in the gene upstream region plays regulatory role under repression. On this nucleosome, the changes in H3K9 and H3K14 acetylations show different dynamics. During repression, acetylation levels on H3K9 show steady increase whereas H3K14 acetylation increases with a peak at 40 min after which levels reduce. Both the levels settle by 2 hr to a level higher than the active state, which revert to normal levels with nutrient repletion. The increase in H3 acetylations is seen in the mutants reported to show reduced SNR6 transcription but not in the maf1Δ cells. This increase on a regulatory nucleosome may be part of the signaling mechanisms, which prepare cells for the stress-related quick repression as well as reactivation. The contrasting association of the histone acetylations with pol II and pol III transcription may be an important consideration to make in research studies focused on drug developments targeting histone modifications.
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Affiliation(s)
| | - Ashutosh Shukla
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Ashis Kumar Pradhan
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Purnima Bhargava
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India.
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5
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Li X, Shen K, Yuan D, Fan J, Yang Y, Tian F, Quan J, Li C, Wang J. Sodium arsenite exposure enhances H3K14 acetylation and impairs male spermatogenesis in rat testes. Reprod Toxicol 2023; 122:108474. [PMID: 37757915 DOI: 10.1016/j.reprotox.2023.108474] [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: 05/13/2023] [Revised: 08/26/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023]
Abstract
Histone modifications play important roles in the epigenetic regulation of spermatogenesis via mediating gene transcription. Steroidogenic regulatory enzymes control testosterone biosynthesis, which are essential for spermatogenesis. Arsenic exposure inhibits the expression of steroidogenic genes by significantly increasing tri-methylation of H3K9 (H3K9me3) level in rat testis, finally diminishes testosterone release and lowers the rat sperm quality. Acetylation of H3K14 (H3K14ac) is associated with testosterone production and spermatogenesis. Co-occurrence of H3K9me3/H3K14ac has been identified previously by mass spectrometry in histone H3 isolated from different human cell types. H3K9me3/H3K14ac dually marked regions are in a poised inactive state to inhibit the gene expression. Whereas, whether inorganic arsenic exposure affects spermatogenesis and steroidogenic regulatory enzymes via mediating H3K14ac level has not been studied. Thereupon, the male Sprague-Dawley (SD) rats were exposed to (NaAsO2) for 6 weeks, then the sperm density and motility, testosterone level in serum, arsenic in rat testis were detected. mRNA expression of steroidogenic regulatory enzymes Star, Cyp11a1, Hsd3b and Hsd17b were determined by RT-PCR. H3K14ac level and the expression of histone acetylases of H3K14 (KAT2A and EP300), histone deacetylases of H3K14 (HDAC6 and HDAC3), the reader of H3K14ac (BAZ2A) were determined. The results suggested arsenic enhances H3K14ac in rat testis, which was associated with repression of steroidogenic regulatory genes expression, further reduced testosterone production, and impaired the spermatogenesis.
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Affiliation(s)
- Xiangli Li
- School of Public Health, Lanzhou University, Lanzhou 730030, China
| | - Kaina Shen
- School of Public Health, Lanzhou University, Lanzhou 730030, China
| | - Dunxuan Yuan
- School of Public Health, Lanzhou University, Lanzhou 730030, China
| | - Jinping Fan
- School of Public Health, Lanzhou University, Lanzhou 730030, China
| | - Yan Yang
- School of Public Health, Lanzhou University, Lanzhou 730030, China
| | - Fangzhou Tian
- School of Public Health, Lanzhou University, Lanzhou 730030, China
| | - Jinrou Quan
- School of Public Health, Lanzhou University, Lanzhou 730030, China
| | - Chengyun Li
- School of Public Health, Lanzhou University, Lanzhou 730030, China
| | - Junling Wang
- School of Public Health, Lanzhou University, Lanzhou 730030, China.
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Jiang N, Li W, Jiang S, Xie M, Liu R. Acetylation in pathogenesis: Revealing emerging mechanisms and therapeutic prospects. Biomed Pharmacother 2023; 167:115519. [PMID: 37729729 DOI: 10.1016/j.biopha.2023.115519] [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: 07/18/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023] Open
Abstract
Protein acetylation modifications play a central and pivotal role in a myriad of biological processes, spanning cellular metabolism, proliferation, differentiation, apoptosis, and beyond, by effectively reshaping protein structure and function. The metabolic state of cells is intricately connected to epigenetic modifications, which in turn influence chromatin status and gene expression patterns. Notably, pathological alterations in protein acetylation modifications are frequently observed in diseases such as metabolic syndrome, cardiovascular disorders, and cancer. Such abnormalities can result in altered protein properties and loss of function, which are closely associated with developing and progressing related diseases. In recent years, the advancement of precision medicine has highlighted the potential value of protein acetylation in disease diagnosis, treatment, and prevention. This review includes provocative and thought-provoking papers outlining recent breakthroughs in acetylation modifications as they relate to cardiovascular disease, mitochondrial metabolic regulation, liver health, neurological health, obesity, diabetes, and cancer. Additionally, it covers the molecular mechanisms and research challenges in understanding the role of acetylation in disease regulation. By summarizing novel targets and prognostic markers for the treatment of related diseases, we aim to contribute to the field. Furthermore, we discuss current hot topics in acetylation research related to health regulation, including N4-acetylcytidine and liquid-liquid phase separation. The primary objective of this review is to provide insights into the functional diversity and underlying mechanisms by which acetylation regulates proteins in disease contexts.
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Affiliation(s)
- Nan Jiang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Wenyong Li
- School of Biology and Food Engineering, Fuyang Normal University, Fuyang, Anhui 236037, China
| | - Shuanglin Jiang
- School of Biology and Food Engineering, Fuyang Normal University, Fuyang, Anhui 236037, China
| | - Ming Xie
- North China Petroleum Bureau General Hospital, Renqiu 062550, China.
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
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7
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Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7. Cell Rep 2023; 42:111980. [PMID: 36641753 DOI: 10.1016/j.celrep.2022.111980] [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: 02/25/2019] [Revised: 09/30/2022] [Accepted: 12/23/2022] [Indexed: 01/16/2023] Open
Abstract
In the conventional model of transcriptional activation, transcription factors bind to response elements and recruit co-factors, including histone acetyltransferases. Contrary to this model, we show that the histone acetyltransferase KAT7 (HBO1/MYST2) is required genome wide for histone H3 lysine 14 acetylation (H3K14ac). Examining neural stem cells, we find that KAT7 and H3K14ac are present not only at transcribed genes but also at inactive genes, intergenic regions, and in heterochromatin. KAT7 and H3K14ac were not required for the continued transcription of genes that were actively transcribed at the time of loss of KAT7 but indispensable for the activation of repressed genes. The absence of KAT7 abrogates neural stem cell plasticity, diverse differentiation pathways, and cerebral cortex development. Re-expression of KAT7 restored stem cell developmental potential. Overexpression of KAT7 enhanced neuron and oligodendrocyte differentiation. Our data suggest that KAT7 prepares chromatin for transcriptional activation and is a prerequisite for gene activation.
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Faragó A, Zsindely N, Farkas A, Neller A, Siági F, Szabó MR, Csont T, Bodai L. Acetylation State of Lysine 14 of Histone H3.3 Affects Mutant Huntingtin Induced Pathogenesis. Int J Mol Sci 2022; 23:15173. [PMID: 36499499 PMCID: PMC9738228 DOI: 10.3390/ijms232315173] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Huntington's Disease (HD) is a fatal neurodegenerative disorder caused by the expansion of a polyglutamine-coding CAG repeat in the Huntingtin gene. One of the main causes of neurodegeneration in HD is transcriptional dysregulation that, in part, is caused by the inhibition of histone acetyltransferase (HAT) enzymes. HD pathology can be alleviated by increasing the activity of specific HATs or by inhibiting histone deacetylase (HDAC) enzymes. To determine which histone's post-translational modifications (PTMs) might play crucial roles in HD pathology, we investigated the phenotype-modifying effects of PTM mimetic mutations of variant histone H3.3 in a Drosophila model of HD. Specifically, we studied the mutations (K→Q: acetylated; K→R: non-modified; and K→M: methylated) of lysine residues K9, K14, and K27 of transgenic H3.3. In the case of H3.3K14Q modification, we observed the amelioration of all tested phenotypes (viability, longevity, neurodegeneration, motor activity, and circadian rhythm defects), while H3.3K14R had the opposite effect. H3.3K14Q expression prevented the negative effects of reduced Gcn5 (a HAT acting on H3K14) on HD pathology, while it only partially hindered the positive effects of heterozygous Sirt1 (an HDAC acting on H3K14). Thus, we conclude that the Gcn5-dependent acetylation of H3.3K14 might be an important epigenetic contributor to HD pathology.
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Affiliation(s)
- Anikó Faragó
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Anita Farkas
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Alexandra Neller
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Fruzsina Siági
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Márton Richárd Szabó
- Department of Biochemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary
| | - Tamás Csont
- Department of Biochemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Interdisciplinary Centre of Excellence, University of Szeged, H-6720 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
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Nie Q, Huan X, Kang J, Yin J, Zhao J, Li Y, Zhang Z. MG149 Inhibits MOF-Mediated p53 Acetylation to Attenuate X-Ray Radiation-Induced Apoptosis in H9c2 Cells. Radiat Res 2022; 198:590-598. [PMID: 36481803 DOI: 10.1667/rade-22-00049.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 09/30/2022] [Indexed: 12/13/2022]
Abstract
Cardiomyocyte apoptosis is involved in the pathogenesis of radiation-induced heart disease, but the underlying epigenetic mechanism remains elusive. We evaluated the potential mediating role of males absent on the first (MOF) in the association between epigenetic activation of p53 lysine 120 (p53K120) and X-ray radiation-induced apoptosis in H9c2 cells. H9c2 cells were pretreated for 24 h with the MOF inhibitor MG149 after 4 Gy irradiation, followed by assessment of cell proliferation, injury, and apoptosis. MOF expression was upregulated by X-ray radiation. MG149 suppressed the proliferation inhibition, reduction of mitochondrial membrane potential, ROS production, and cell apoptosis. MG149 may promote the survival of H9c2 cells via inhibition of MOF-mediated p53K120 acetylation in response to X-ray radiation-induced apoptosis. Our data indicates a MOF-associated epigenetic mechanism in H9c2 cells that promotes attenuation of X-ray radiation-induced injury.
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Affiliation(s)
- Qianwen Nie
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China.,Department of General Medicine, Second Hospital of Lanzhou University, No.82 Cui Ying Men, Cheng Guan District, Lanzhou 730030, China
| | - Xuan Huan
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China.,Department of General Medicine, Second Hospital of Lanzhou University, No.82 Cui Ying Men, Cheng Guan District, Lanzhou 730030, China
| | - Jing Kang
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China.,Department of General Medicine, Second Hospital of Lanzhou University, No.82 Cui Ying Men, Cheng Guan District, Lanzhou 730030, China
| | - Jiangyan Yin
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China.,Department of General Medicine, Second Hospital of Lanzhou University, No.82 Cui Ying Men, Cheng Guan District, Lanzhou 730030, China
| | - Jiahui Zhao
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China
| | - Yi Li
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - ZhengYi Zhang
- Lanzhou University Second College of Clinical Medicine, Chengguan District, Lanzhou 730030, China.,Department of General Medicine, Second Hospital of Lanzhou University, No.82 Cui Ying Men, Cheng Guan District, Lanzhou 730030, China
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10
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Ma H, Li L, Gai Y, Zhang X, Chen Y, Zhuo X, Cao Y, Jiao C, Gmitter FG, Li H. Histone Acetyltransferases and Deacetylases Are Required for Virulence, Conidiation, DNA Damage Repair, and Multiple Stresses Resistance of Alternaria alternata. Front Microbiol 2021; 12:783633. [PMID: 34880849 PMCID: PMC8645686 DOI: 10.3389/fmicb.2021.783633] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/02/2021] [Indexed: 01/16/2023] Open
Abstract
Histone acetylation, which is critical for transcriptional regulation and various biological processes in eukaryotes, is a reversible dynamic process regulated by HATs and HDACs. This study determined the function of 6 histone acetyltransferases (HATs) (Gcn5, RTT109, Elp3, Sas3, Sas2, Nat3) and 6 histone deacetylases (HDACs) (Hos2, Rpd3, Hda1, Hos3, Hst2, Sir2) in the phytopathogenic fungus Alternaria alternata by analyzing targeted gene deletion mutants. Our data provide evidence that HATs and HDACs are both required for mycelium growth, cell development and pathogenicity as many gene deletion mutants (ΔGcn5, ΔRTT109, ΔElp3, ΔSas3, ΔNat3, ΔHos2, and ΔRpd3) displayed reduced growth, conidiation or virulence at varying degrees. In addition, HATs and HDACs are involved in the resistance to multiple stresses such as oxidative stress (Sas3, Gcn5, Elp3, RTT109, Hos2), osmotic stress (Sas3, Gcn5, RTT109, Hos2), cell wall-targeting agents (Sas3, Gcn5, Hos2), and fungicide (Gcn5, Hos2). ΔGcn5, ΔSas3, and ΔHos2 displayed severe growth defects on sole carbon source medium suggesting a vital role of HATs and HDACs in carbon source utilization. More SNPs were generated in ΔGcn5 in comparison to wild-type when they were exposed to ultraviolet ray. Moreover, ΔRTT109, ΔGcn5, and ΔHos2 showed severe defects in resistance to DNA-damaging agents, indicating the critical role of HATs and HDACs in DNA damage repair. These phenotypes correlated well with the differentially expressed genes in ΔGcn5 and ΔHos2 that are essential for carbon sources metabolism, DNA damage repair, ROS detoxification, and asexual development. Furthermore, Gcn5 is required for the acetylation of H3K4. Overall, our study provides genetic evidence to define the central role of HATs and HDACs in the pathological and biological functions of A. alternata.
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Affiliation(s)
- Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China.,Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China.,Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Lei Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yunpeng Gai
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaoyan Zhang
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yanan Chen
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaokang Zhuo
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yingzi Cao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chen Jiao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fred G Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Hongye Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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11
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Breakers and amplifiers in chromatin circuitry: acetylation and ubiquitination control the heterochromatin machinery. Curr Opin Struct Biol 2021; 71:156-163. [PMID: 34303934 PMCID: PMC8667873 DOI: 10.1016/j.sbi.2021.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/06/2021] [Accepted: 06/13/2021] [Indexed: 11/30/2022]
Abstract
Eukaryotic genomes are segregated into active euchromatic and repressed heterochromatic compartments. Gene regulatory networks, chromosomal structures, and genome integrity rely on the timely and locus-specific establishment of active and silent states to protect the genome and provide the basis for cell division and specification of cellular identity. Here, we focus on the mechanisms and molecular machinery that establish heterochromatin in Schizosaccharomyces pombe and compare it with Saccharomyces cerevisiae and the mammalian polycomb system. We present recent structural and mechanistic evidence, which suggests that histone acetylation protects active transcription by disrupting the positive feedback loops used by the heterochromatin machinery and that H2A and H3 monoubiquitination actively drives heterochromatin, whereas H2B monoubiquitination mobilizes the defenses to quench heterochromatin. Heterochromatin-associated complexes are attracted and repelled by histone marks. Acetylation of specific lysine residues protects euchromatin from silencing. Methylation of histone H3 lysine 9 and 27 amplifies heterochromatin. Nucleosome ubiquitination licences and enforces feedback loops.
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12
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Nevil M, Duronio RJ. The awesome power of histone genetics. Mol Cell 2021; 81:1593-1595. [PMID: 33861947 PMCID: PMC9531585 DOI: 10.1016/j.molcel.2021.03.023] [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: 11/19/2022]
Abstract
Using a genetic platform to generate histone mutants in Drosophila, Regadas et al. (2021) discover a novel mechanism for tissue-specific gene expression requiring a chromatin state defined by acetylation of lysine 14 of H3 but lacking other activating histone post-translational modifications.
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Affiliation(s)
- Markus Nevil
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; SPIRE, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA; Departments of Biology and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
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13
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Regadas I, Dahlberg O, Vaid R, Ho O, Belikov S, Dixit G, Deindl S, Wen J, Mannervik M. A unique histone 3 lysine 14 chromatin signature underlies tissue-specific gene regulation. Mol Cell 2021; 81:1766-1780.e10. [PMID: 33631105 DOI: 10.1016/j.molcel.2021.01.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 12/13/2022]
Abstract
Organismal development and cell differentiation critically depend on chromatin state transitions. However, certain developmentally regulated genes lack histone 3 lysine 9 and 27 acetylation (H3K9ac and H3K27ac, respectively) and histone 3 lysine 4 (H3K4) methylation, histone modifications common to most active genes. Here we describe a chromatin state featuring unique histone 3 lysine 14 acetylation (H3K14ac) peaks in key tissue-specific genes in Drosophila and human cells. Replacing H3K14 in Drosophila demonstrates that H3K14 is essential for expression of genes devoid of canonical histone modifications in the embryonic gut and larval wing imaginal disc, causing lethality and defective wing patterning. We find that the SWI/SNF protein Brahma (Brm) recognizes H3K14ac, that brm acts in the same genetic pathway as H3K14R, and that chromatin accessibility at H3K14ac-unique genes is decreased in H3K14R mutants. Our results show that acetylation of a single lysine is essential at genes devoid of canonical histone marks and uncover an important requirement for H3K14 in tissue-specific gene regulation.
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Affiliation(s)
- Isabel Regadas
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Olle Dahlberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Roshan Vaid
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Oanh Ho
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75237, Uppsala, Sweden
| | - Sergey Belikov
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Gunjan Dixit
- Department of Genome Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75237, Uppsala, Sweden
| | - Jiayu Wen
- Department of Genome Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia.
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden.
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14
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Yokota K, Shibata H, Kurihara I, Kobayashi S, Murai-Takeda A, Itoh H. CASZ1b is a novel transcriptional corepressor of mineralocorticoid receptor. Hypertens Res 2020; 44:407-416. [DOI: 10.1038/s41440-020-00562-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022]
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15
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Lin J, Hung FY, Ye C, Hong L, Shih YH, Wu K, Li QQ. HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis. Genome Res 2020; 30:1407-1417. [PMID: 32759225 PMCID: PMC7605263 DOI: 10.1101/gr.255232.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 07/28/2020] [Indexed: 12/21/2022]
Abstract
Eukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs). Although nucleosomes have been reported to regulate mRNA polyadenylation in humans, the role of HDACs in regulating polyadenylation has not been uncovered. Taking advantage of phenotypic studies on Arabidopsis, HDA6 (one of HDACs) was found to be a critical part of many biological processes. Here, we report that HDA6 affects mRNA polyadenylation in Arabidopsis. Poly(A) sites of up-regulated transcripts are closer to the histone acetylation peaks in hda6 compared to the wild-type Col-0. HDA6 is required for the deacetylation of histones around DNA on nucleosomes, which solely coincides with up-regulated or uniquely presented poly(A) sites in hda6. Furthermore, defective HDA6 results in an overrepresentation of the canonical poly(A) signal (AAUAAA) usage. Chromatin loci for generating AAUAAA-type transcripts have a comparatively low H3K9K14ac around poly(A) sites when compared to other noncanonical poly(A) signal–containing transcripts. These results indicate that HDA6 regulates polyadenylation in a histone deacetylation–dependent manner in Arabidopsis.
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Affiliation(s)
- Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan 10617
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Liwei Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Yuan-Hsin Shih
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan 10617
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan 10617
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California 91766, USA
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16
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Dynamic regulation of histone H3 lysine (K) acetylation and deacetylation during prolonged oxygen deprivation in a champion anaerobe. Mol Cell Biochem 2020; 474:229-241. [PMID: 32729004 DOI: 10.1007/s11010-020-03848-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022]
Abstract
Trachemys scripta elegans can survive up to three months of absolute anoxia at 3 °C and recover with minimal cellular damage. Red-eared sliders employ various physiological and biochemical adaptations to survive anoxia with metabolic rate depression (MRD) being the most prominent adaptation. MRD is mediated by epigenetic, transcriptional, post-transcriptional, and post-translational mechanisms aimed at shutting down cellular processes that are not needed for anoxia survival, while reprioritizing ATP towards cell processes that are vital for anaerobiosis. Histone acetylation/deacetylation are epigenetic modifications that maintain a proper balance between permissive chromatin and restricted chromatin, yet very little is known about protein regulation and enzymatic activity of the writers and erasers of acetylation during natural anoxia tolerance. As such, this study explored the interplay between transcriptional activators, histone acetyltransferases (HATs), and transcriptional repressors, sirtuins (SIRTs), along with three prominent acetyl-lysine (K) moieties of histone H3 in the liver of red-eared sliders. Western immunoblotting was used to measure acetylation levels of H3-K14, H3-K18, and H3-K56, as well as protein levels of histone H3-total, HATs, and nuclear SIRTs in the liver in response to 5 h and 20 h anoxia. Global and nuclear enzymatic activity of HATs and enzymatic activity of nuclear SIRTs were also measured. Overall, a strong suppression of HATs-mediated H3 acetylation and SIRT-mediated deacetylation was evident in the liver of red-eared sliders that could play an important role in ATP conservation as part of the overall reduction in metabolic rate.
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17
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Gong X, Yu Q, Duan K, Tong Y, Zhang X, Mei Q, Lu L, Yu X, Li S. Histone acetyltransferase Gcn5 regulates gene expression by promoting the transcription of histone methyltransferase SET1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194603. [PMID: 32663628 DOI: 10.1016/j.bbagrm.2020.194603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/20/2020] [Accepted: 07/08/2020] [Indexed: 01/26/2023]
Abstract
Many chromatin modifying factors regulate gene expression in an as-yet-unknown indirect manner. Revealing the molecular basis for this indirect gene regulation will help understand their precise roles in gene regulation and associated biological processes. Here, we studied histone modifying enzymes that indirectly regulate gene expression by modulating the expression of histone methyltransferase, Set1. Through unbiased screening of the histone H3/H4 mutant library, we identified 13 histone substitution mutations with reduced levels of Set1 and H3K4 trimethylation (H3K4me3) and 2 mutations with increased levels of Set1 and H3K4me3, which concentrate at 3 structure clusters. Among these substitutions, the H3K14A mutant substantially reduces SET1 transcription and H3K4me3. H3K14 is acetylated by histone acetyltransferase Gcn5 at SET1 promoter, which then promotes SET1 transcription to maintain normal H3K4me3 levels. In contrast, the histone deacetylase Rpd3 deacetylates H3K14 to repress SET1 transcription and hence reduce H3K4me3 levels, establishing a dynamic crosstalk between H3K14ac and H3K4me3. By promoting the transcription of SET1 and maintaining H3K4me3 levels, Gcn5 regulates the transcription of a subset gene in an indirect manner. Collectively, we propose a model wherein Gcn5 promotes the expression of chromatin modifiers to regulate histone crosstalk and gene transcription.
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Affiliation(s)
- Xuanyunjing Gong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Kai Duan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yue Tong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Xinyu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qianyun Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Li Lu
- Institute of TCM and Natural Products, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
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18
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Fang YC, Chan L, Liou JP, Tu YK, Lai MJ, Chen CI, Vidyanti AN, Lee HY, Hu CJ. HDAC inhibitor protects chronic cerebral hypoperfusion and oxygen-glucose deprivation injuries via H3K14 and H4K5 acetylation-mediated BDNF expression. J Cell Mol Med 2020; 24:6966-6977. [PMID: 32374084 PMCID: PMC7299713 DOI: 10.1111/jcmm.15358] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
Vascular dementia (VaD) is the second most common cause of dementia, but the treatment is still lacking. Although many studies have reported that histone deacetylase inhibitors (HDACis) confer protective effects against ischemic and hypoxic injuries, their role in VaD is still uncertain. Previous studies shown, one HDACi protected against cognitive decline in animals with chronic cerebral hypoperfusion (CCH). However, the underlying mechanisms remain elusive. In this study, we tested several 10,11‐dihydro‐5H‐dibenzo[b,f]azepine hydroxamates, which act as HDACis in the CCH model (in vivo), and SH‐SY5Y (neuroblastoma cells) with oxygen‐glucose deprivation (OGD, in vitro). We identified a compound 13, which exhibited the best cell viability under OGD. The compound 13 could increase, in part, the protein levels of brain‐derived neurotrophic factor (BDNF). It increased acetylation status on lysine 14 residue of histone 3 (H3K14) and lysine 5 of histone 4 (H4K5). We further clarified which promoters (I, II, III, IV or IX) could be affected by histone acetylation altered by compound 13. The results of chromatin immunoprecipitation and Q‐PCR analysis indicate that an increase in H3K14 acetylation leads to an increase in the expression of BDNF promoter II, while an increase in H4K5 acetylation results in an increase in the activity of BDNF promoter II and III. Afterwards, these cause an increase in the expression of BDNF exon II, III and coding exon IX. In summary, the HDACi compound 13 may increase BDNF specific isoforms expression to rescue the ischemic and hypoxic injuries through changes of acetylation on histones.
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Affiliation(s)
- Yao-Ching Fang
- Taipei Neuroscience Institute, Taipei Medical University, Taipei, Taiwan
| | - Lung Chan
- Department of Neurology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Jing-Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.,TMU Biomedical Commercialization Center, Taipei Medical University, Taipei, Taiwan
| | - Yong-Kwang Tu
- Taipei Neuroscience Institute, Taipei Medical University, Taipei, Taiwan.,Department of Neurology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Mei-Jung Lai
- TMU Biomedical Commercialization Center, Taipei Medical University, Taipei, Taiwan
| | - Chin-I Chen
- Department of Neurology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Amelia Nur Vidyanti
- Department of Neurology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,International Master/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hsueh-Yun Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Chaur-Jong Hu
- Taipei Neuroscience Institute, Taipei Medical University, Taipei, Taiwan.,Department of Neurology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
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19
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Li Y, Sun W, Sun D, Yin D. Retracted: Ras-ERK1/2 signaling promotes the development of uveal melanoma by downregulating H3K14ac. J Cell Physiol 2019; 234:16011-16020. [PMID: 30770563 DOI: 10.1002/jcp.28259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/17/2019] [Accepted: 01/22/2019] [Indexed: 01/24/2023]
Abstract
Ras-extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) signaling has been proposed as the crucial regulators in the development of various cancers. Histone acetylation at H3 lysine 14 (H3K14ac) is closely associated with gene expression and DNA damage. However, whether H3K14ac participates in mediating Ras-ERK1/2-induced cell proliferation and migration in uveal melanoma cells remains unknown. The purpose of this study is to investigate the effect of H3K14ac on Ras-ERK1/2 affected uveal melanoma cell phenotypes. MP65 cells were transfected with Ras WT and Ras G12V/T35S , the unloaded plasmid of pEGFP-N1 served as a negative control. Protein levels of phosphorylated ERK1/2 Thr202 and H3K14ac were assessed by western blot assay. Cell viability, number of colonies, migration, and the downstream genes of ERK1/2 were analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2-H-tetrazolium bromide, soft-agar colony formation, transwell, and chromatin immunoprecipitation assays. HA-tag vectors of CLR3 and TIP60 and the small interfering RNAs that specific for CLR3 and MDM2 were transfected into MP65 cells to uncover the effects of CLR3, TIP60, and MDM2 on Ras-ERK1/2 mediated H3K14ac expression and MP65 cell phenotypes. We found that, Ras-ERK1/2 decreased H3K14ac expression in MP65 cells, and H3K14ac significantly suppressed Ras-ERK1/2-induced cell viability, colony formation, and migration in MP65 cells. Moreover, the transcription of CYR61, IGFBP3, WNT16B, NT5E, GDF15, and CARD16 was regulated by H3K14ac. Additionally, CLR3 silence recovered H3K14ac expression and reversed the effect of Ras-ERK1/2 on MP65 cell proliferation, migration and the mRNAs of ERK1/2 downstream genes. Besides, Ras-ERK1/2 decreased H3K14ac expression by MDM2-mediated TIP60 degradation. In conclusion, Ras-ERK1/2 promoted uveal melanoma cells growth and migration by downregulating H3K14ac via MDM2-mediated TIP60 degradation.
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Affiliation(s)
- Yaping Li
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China
| | - Weixuan Sun
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Dajun Sun
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Dexin Yin
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
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20
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TASks for subtelomeres: when nucleosome loss and genome instability are favored. Curr Genet 2019; 65:1153-1160. [DOI: 10.1007/s00294-019-00986-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 10/26/2022]
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21
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Porter EG, Dhiman A, Chowdhury B, Carter BC, Lin H, Stewart JC, Kazemian M, Wendt MK, Dykhuizen EC. PBRM1 Regulates Stress Response in Epithelial Cells. iScience 2019; 15:196-210. [PMID: 31077944 PMCID: PMC6514269 DOI: 10.1016/j.isci.2019.04.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 03/10/2019] [Accepted: 04/19/2019] [Indexed: 12/16/2022] Open
Abstract
Polybromo1 (PBRM1) is a chromatin remodeler subunit highly mutated in cancer, particularly clear cell renal carcinoma. PBRM1 is a member of the SWI/SNF subcomplex, PBAF (PBRM1-Brg1/Brm-associated factors), and is characterized by six tandem bromodomains. Here we establish a role for PBRM1 in epithelial cell maintenance through the expression of genes involved in cell adhesion, metabolism, stress response, and apoptosis. In support of a general role for PBRM1 in stress response and apoptosis, we observe that loss of PBRM1 results in an increase in reactive oxygen species generation and a decrease in cellular viability under stress conditions. We find that loss of PBRM1 promotes cell growth under favorable conditions but is required for cell survival under conditions of cellular stress. PBRM1 facilitates the expression of stress response genes in epithelial cells Deletion of PBRM1 promotes growth under low-stress conditions PBRM1 restrains ROS generation and induces apoptosis under high-stress conditions Under H2O2 stress, PBRM1 cooperates with cJun and NRF2 to induce gene expression
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Affiliation(s)
- Elizabeth G Porter
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA
| | - Basudev Chowdhury
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA
| | - Benjamin C Carter
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA
| | - Hang Lin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA
| | - Jane C Stewart
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | - Michael K Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA.
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22
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West KL, Byrum SD, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ. Proteomic characterization of the arsenic response locus in S. cerevisiae. Epigenetics 2019; 14:130-145. [PMID: 30739529 PMCID: PMC6557609 DOI: 10.1080/15592294.2019.1580110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 01/17/2019] [Accepted: 01/21/2019] [Indexed: 10/27/2022] Open
Abstract
Arsenic exposure is a global health problem. Millions of people encounter arsenic through contaminated drinking water, consumption, and inhalation. The arsenic response locus in budding yeast is responsible for the detoxification of arsenic and its removal from the cell. This locus constitutes a conserved pathway ranging from prokaryotes to higher eukaryotes. The goal of this study was to identify how transcription from the arsenic response locus is regulated in an arsenic dependent manner. An affinity enrichment strategy called CRISPR-Chromatin Affinity Purification with Mass Spectrometry (CRISPR-ChAP-MS) was used, which provides for the proteomic characterization of a targeted locus. CRISPR-ChAP-MS was applied to the promoter regions of the activated arsenic response locus and uncovered 40 nuclear-annotated proteins showing enrichment. Functional assays identified the histone acetyltransferase SAGA and the chromatin remodelling complex SWI/SNF to be required for activation of the locus. Furthermore, SAGA and SWI/SNF were both found to specifically organize the chromatin structure at the arsenic response locus for activation of gene transcription. This study provides the first proteomic characterization of an arsenic response locus and key insight into the mechanisms of transcriptional activation that are necessary for detoxification of arsenic from the cell.
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Affiliation(s)
- Kirk L. West
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephanie D. Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children’s Research Institute, Little Rock, AR, USA
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Rick D. Edmondson
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan J. Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children’s Research Institute, Little Rock, AR, USA
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23
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Ma F, Jiang S, Zhang CY. Recent advances in histone modification and histone modifying enzyme assays. Expert Rev Mol Diagn 2018; 19:27-36. [DOI: 10.1080/14737159.2019.1559053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fei Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
| | - Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, China
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24
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Watts BR, Wittmann S, Wery M, Gautier C, Kus K, Birot A, Heo DH, Kilchert C, Morillon A, Vasiljeva L. Histone deacetylation promotes transcriptional silencing at facultative heterochromatin. Nucleic Acids Res 2018; 46:5426-5440. [PMID: 29618061 PMCID: PMC6009587 DOI: 10.1093/nar/gky232] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/25/2022] Open
Abstract
It is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in heterochromatin these genes are transcribed and believed to be repressed primarily at the level of RNA. However, the mechanism of facultative heterochromatin formation and the interplay with transcription regulation is not understood. We show genome-wide that HDAC-dependent histone deacetylation is a major determinant in transcriptional silencing of facultative heterochromatin domains. Indeed, mutation of class I/II HDACs leads to increased transcription of meiotic genes and accumulation of their mRNAs. Mechanistic dissection of the pho1 gene where, in response to phosphate, transient facultative heterochromatin is established by overlapping lncRNA transcription shows that the Clr3 HDAC contributes to silencing independently of SHREC, but in an lncRNA-dependent manner. We propose that HDACs promote facultative heterochromatin by establishing alternative transcriptional silencing.
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Affiliation(s)
- Beth R Watts
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Maxime Wery
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Camille Gautier
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Krzysztof Kus
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Adrien Birot
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Dong-Hyuk Heo
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Cornelia Kilchert
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Institut für Biochemie, Heinrich-Buff-Ring 17, 35392 Gießen, Germany
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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Cai Q, Wang JJ, Fu B, Ying SH, Feng MG. Gcn5-dependent histone H3 acetylation and gene activity is required for the asexual development and virulence of Beauveria bassiana. Environ Microbiol 2018; 20:1484-1497. [PMID: 29417710 DOI: 10.1111/1462-2920.14066] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 12/11/2022]
Abstract
Gcn5 is a core histone acetyltransferase that catalyzes histone H3 acetylation on N-terminal lysine residues in yeasts and was reported to catalyze H3K9/K14 acetylation required for activating asexual development in Aspergillus. Here, we report a localization of Gcn5 ortholog in the nucleus and cytoplasm of Beauveria bassiana, a fungal insect pathogen. Deletion of gcn5 led to hypoacetylated H3 at K9/14/18/27 and 97% reduction in conidiation capacity as well as severe defects in colony growth and conidial thermotolerance. Two master conidiation genes, namely brlA and abaA, were transcriptionally repressed to undetectable level in Δgcn5, but sharply upregulated in wild-type, at the beginning time of conidiation. Based on chromatin immunoprecipitation, both DNA and acetylation levels of the distal and proximal fragments of the brlA promoter bound by acetylated H3K14 alone were upregulated in wild-type, but not in Δgcn5, at the mentioned time. In Δgcn5, normal cuticle infection was abolished while virulence through cuticle-bypassing infection was greatly attenuated, accompanied by drastically reduced activities of putative cuticle-degrading enzymes, retarded dimorphic transition and transcriptional repression of associated genes. These findings unveil a novel mechanism by which Gcn5 activates asexual development pathway by acetylating H3K14 and regulates the virulence-related cellular events in B. bassiana.
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Affiliation(s)
- Qing Cai
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Juan-Juan Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China.,School of Biological Science and Biotechnology, University of Jinan, Jinan, Shandong, 250022, People's Republic of China
| | - Bo Fu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
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Qi S, He L, Zhang Q, Dong Q, Wang Y, Yang Q, Tian C, He Q, Wang Y. Cross-pathway control gene CPC1/GCN4 coordinates with histone acetyltransferase GCN5 to regulate catalase-3 expression under oxidative stress in Neurospora crassa. Free Radic Biol Med 2018; 117:218-227. [PMID: 29421311 DOI: 10.1016/j.freeradbiomed.2018.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/04/2018] [Accepted: 02/02/2018] [Indexed: 12/16/2022]
Abstract
Catalase is an important enzyme found in nearly all aerobic organisms and plays an essential role in protecting cells from oxidative damage by catalyzing the degradation of hydrogen peroxide into water and oxygen. In filamentous fungus Neurospora crassa, the expression levels of catalases are rigorously regulated by morphogenetic transition during growth and development in cells. Our study revealed that catalase-3 transcription is positively regulated by histone acetyltransferase GCN5 and the cross-pathway control gene cpc-1, as the cat-3 expression level is significantly decreased in gcn5KO and cpc-1 (j-5) mutants. Moreover, gcn5KO and cpc-1 (j-5) mutants could not respond to H2O2 treatment due to the inadequate cat-3 transcription, while wild-type strains showed high expression levels of catalase upon H2O2 treatment. The global H3 acetylation and the acetylation of H3 at cat-3 locus dramatically decreased in gcn5KO under normal or oxidative stress conditions. Meanwhile, the expression of CAT-3 is reduced in gcn5E146Q, the catalytically dead mutant, suggesting that the catalytic activity of GCN5 functions in regulation of cat-3 transcription. In addition, GCN5 cannot acetylate histone H3 efficiently at cat-3 locus in cpc-1 (j-5) mutant strains under normal or oxidative stress conditions. Furthermore, ChIP assays data revealed that the CPC1/GCN4 can directly target the cat-3 promoter region, which may recruit GCN5 to modify the histone acetylation of this region. These results disclosed a distinctive function of CPC1/GCN4 in the regulatory pathway of cat-3 transcription, which is mediated by GCN5-dependent acetylation.
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Affiliation(s)
- Shaohua Qi
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lingaonan He
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qin Zhang
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qing Dong
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yajun Wang
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qiuying Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chaoguang Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qun He
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ying Wang
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Role of influenza A virus NP acetylation on viral growth and replication. Nat Commun 2017; 8:1259. [PMID: 29097654 PMCID: PMC5668263 DOI: 10.1038/s41467-017-01112-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/17/2017] [Indexed: 12/29/2022] Open
Abstract
Lysine acetylation is a post-translational modification known to regulate protein functions. Here we identify several acetylation sites of the influenza A virus nucleoprotein (NP), including the lysine residues K77, K113 and K229. Viral growth of mutant virus encoding K229R, mimicking a non-acetylated NP lysine residue, is severely impaired compared to wildtype or the mutant viruses encoding K77R or K113R. This attenuation is not the result of decreased polymerase activity, altered protein expression or disordered vRNP co-segregation but rather caused by impaired particle release. Interestingly, release deficiency is also observed mimicking constant acetylation at this site (K229Q), whereas virus encoding NP-K113Q could not be generated. However, mimicking NP hyper-acetylation at K77 and K229 severely diminishes viral polymerase activity, while mimicking NP hypo-acetylation at these sites has no effect on viral replication. These results suggest that NP acetylation at K77, K113 and K229 impacts multiple steps in viral replication of influenza A viruses. Post-translational modifications of influenza A virus proteins can regulate virus replication, but the effect of nucleoprotein (NP) acetylation is not known. Here, Giese et al. identify four NP lysine residues that are acetylated in infected cells and study their role in polymerase activity and virion release.
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Wu J, Liu C, Zhang L, Qu CH, Sui XL, Zhu H, Huang L, Xu YF, Han YL, Qin C. Histone deacetylase-2 is involved in stress-induced cognitive impairment via histone deacetylation and PI3K/AKT signaling pathway modification. Mol Med Rep 2017; 16:1846-1854. [PMID: 28656275 PMCID: PMC5561802 DOI: 10.3892/mmr.2017.6840] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 03/07/2017] [Indexed: 12/24/2022] Open
Abstract
Exposure to chronic stress upregulates blood glucocorticoid levels and impairs cognition via diverse epigenetic mechanisms, such as histone deacetylation. Histone deacetylation can lead to transcriptional silencing of many proteins involved in cognition and may also cause learning and memory dysfunction. Histone deacetylase-2 (HDAC2) has been demonstrated to epigenetically block cognition via a reduction in the histone acetylation level; however, it is unknown whether HDAC2 is involved in the cognitive decline induced by chronic stress. To the best of authors' knowledge, this is the first study to demonstrate that the stress hormone corticosteroid upregulate HDAC2 protein levels in neuro-2a cells and cause cell injuries. HDAC2 knockdown resulted in a significant amelioration of the pathological changes in N2a cells via the upregulation of histone acetylation and modifications in the phosphoinositide 3-kinase/protein kinase B signaling pathway. In addition, the HDAC2 protein levels were upregulated in 12-month-old female C57BL/6J mice under chronic stress in vivo. Taken together, these findings suggested that HDAC2 may be an important negative regulator involved in chronic stress-induced cognitive impairment.
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Affiliation(s)
- Jie Wu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, P.R. China
| | - Cui Liu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, P.R. China
| | - Ling Zhang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, P.R. China
| | - Chun-Hui Qu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, P.R. China
| | - Xiao-Long Sui
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, P.R. China
| | - Hua Zhu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, P.R. China
| | - Lan Huang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, P.R. China
| | - Yan-Feng Xu
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, P.R. China
| | - Yun-Lin Han
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, P.R. China
| | - Chuan Qin
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, P.R. China
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Xu L, Jia Y, Yang XH, Han F, Zheng Y, Ni Y, Chen X, Hong J, Liu JQ, Li Q, Sun RH, Mo SJ. MicroRNA-130b transcriptionally regulated by histone H3 deacetylation renders Akt ubiquitination and apoptosis resistance to 6-OHDA. Biochim Biophys Acta Mol Basis Dis 2017; 1863:1678-1689. [PMID: 28412322 DOI: 10.1016/j.bbadis.2017.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 04/09/2017] [Accepted: 04/11/2017] [Indexed: 12/12/2022]
Abstract
Apoptosis of DA neurons is a contributing cause of disability and death for Parkinson's disease (PD). Akt may become a potential therapeutic target for PD since Akt has been deactivated during DA neuron apoptosis. We previously demonstrated that Akt confers apoptosis resistance against 6-OHDA in DA neuron-like PC12 cells, yet the underlying mechanisms accounted for this are not fully understood. Here we report that microRNA-130b (miR-130b)-dependent and cylindromatosis (CYLD) repression-mediated Akt ubiquitination renders apoptosis resistance of PC12 cells to 6-OHDA, which elicits histone H3 deacetylation-induced transcriptional downregulation of miR-130b vice versa. CYLD deficiency ubiquitinates Akt at Lys63, thereby phosphorylating Akt and antagonizing 6-OHDA-initiated apoptosis. MiR-130b targetedly represses CYLD and increases apoptosis resistance to 6-OHDA. CYLD repression by miR-130b restores Akt ubiquitination and activation, GSK3β and FoxO3a phosphorylation, FoxO3a removal from Bim promoter as well as Bim downregulation during 6-OHDA administration. CYLD deficiency-mediated Akt activation is instrumental for the apoptosis-resistant phenotypes of miR-130b. In addition, 6-OHDA transcriptionally downregulates miR-130b through recruitment of HDAC3 at the promoter. Furthermore, EPO potentiates the ability of miR-130b to activate Akt and augment apoptosis resistance. Our findings identify the apoptosis-resistant function of miR-130b and suggest that histone H3 deacetylation plays a pivotal role in regulating miR-130b transcription in response to 6-OHDA.
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Affiliation(s)
- Liang Xu
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China
| | - Yu Jia
- Department of Nephrology, Tongji Hospital, Tongji Medical College of Huanzhong University of Science & Technology, Wuhan 430030, Hubei, China
| | - Xiang-Hong Yang
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China
| | - Fang Han
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China
| | - Yang Zheng
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China
| | - Yin Ni
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China
| | - Xu Chen
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China
| | - Jun Hong
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China
| | - Jing-Quan Liu
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China
| | - Qian Li
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China
| | - Ren-Hua Sun
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China.
| | - Shi-Jing Mo
- Department of Critical Care Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310000, Zhejiang, China.
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Metabolism and chromatin dynamics in health and disease. Mol Aspects Med 2017; 54:1-15. [DOI: 10.1016/j.mam.2016.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/22/2016] [Accepted: 09/27/2016] [Indexed: 01/04/2023]
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Perera E, Yúfera M. Effects of soybean meal on digestive enzymes activity, expression of inflammation-related genes, and chromatin modifications in marine fish (Sparus aurata L.) larvae. FISH PHYSIOLOGY AND BIOCHEMISTRY 2017; 43:563-578. [PMID: 27807713 DOI: 10.1007/s10695-016-0310-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
The effects of soybean meal (SBM) in early diet of Sparus aurata larvae at two developmental windows were assessed. Prolonged (beyond 14 days post-hatch, dph) feeding with SBM decreased the activity of pancreatic enzymes of larvae. In the absence of SBM these larvae later resumed enzyme activities, but exhibited a significant delay in development. Larvae response to SBM involved up-regulation of extracellular matrix remodeling enzymes and pro-inflammatory cytokines, coupled with a drop in putative intestinal enzymes. Larvae receiving SBM at first feeding appear later to have lower expression of inflammation-related genes, especially those fed SBM until 14 dph. Multivariate analysis confirmed that the duration of the SBM early feeding period drives the physiology of larvae in different directions. Feeding larvae with SBM increased global histone H3 acetylation, whereas upon removal of SBM the process was reverted. A more in deep analysis revealed a dynamic interplay among several reversible histone modifications such as H3K14ac and H3K27m3. Finally, we showed that SBM feeding of larvae results in global hypomethylation that persist after SBM removal. This study is the first demonstrating an effect of diet on marine fish epigenetics. It is concluded that there are limitations for extending SBM feeding of S. aurata larvae beyond 14 dph even under co-feeding with live feed, affecting key physiological processes and normal growth. However, up to 14 dph, SBM does not affect normal development, and produces apparently lasting effects on some key enzymes, genes, and chromatin modifications.
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Affiliation(s)
- Erick Perera
- Departamento de Biología Marina y Acuicultura, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Puerto Real, 11510, Cádiz, Spain.
- Control of Food Intake Group, Department of Fish Physiology and Biotechnology, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain.
| | - Manuel Yúfera
- Departamento de Biología Marina y Acuicultura, Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Puerto Real, 11510, Cádiz, Spain
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Fei HJ, Zu LD, Wu J, Jiang XS, Wang JL, Chin YE, Fu GH. PCAF acts as a gastric cancer suppressor through a novel PCAF-p16-CDK4 axis. Am J Cancer Res 2016; 6:2772-2786. [PMID: 28042499 PMCID: PMC5199753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 11/29/2016] [Indexed: 06/06/2023] Open
Abstract
Gastric cancer (GC) is a leading cause of cancer-related death worldwide and the pathogenesis of GC remains largely unknown. Here, we demonstrate a novel mechanism by which P300/CBP associating factor (PCAF) acts as a tumor suppressor in GC cells. We showed that both PCAF mRNA and protein were downregulated in GC cells, and that this downregulation correlated with poor survival. Meanwhile, the interaction between human anion exchanger 1 (AE1) and p16 is a key event in GC development. We found that PCAF inhibited GC growth by interacting with AE1 and p16 to promote ubiquitin-mediated degradation of AE1 and p16 upregulation and translocation into the nucleus. Binding of nuclear p16 to CDK4 prevented the CDK4-Cyclin D1 interaction to inhibit GC proliferation. Furthermore, reduced PCAF levels in GC cells were associated with intracellular alkalinization and decreased immunity. Together these results suggest that PCAF acts as a GC suppressor through a novel PCAF-p16-CDK4 axis. The downregulation of PCAF expression in GC cells that follows intracellular alkalinization and decreased immune response, indicates that GC therapies should focus on restoring PCAF levels.
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Affiliation(s)
- Hong-Jun Fei
- Pathology Center, Shanghai General Hospital/Faculty of Basic Medicine, School of Medicine, Shanghai Jiao Tong UniversityShanghai 200025, P. R. China
| | - Li-Dong Zu
- Pathology Center, Shanghai General Hospital/Faculty of Basic Medicine, School of Medicine, Shanghai Jiao Tong UniversityShanghai 200025, P. R. China
| | - Jun Wu
- Pathology Center, Shanghai General Hospital/Faculty of Basic Medicine, School of Medicine, Shanghai Jiao Tong UniversityShanghai 200025, P. R. China
| | - Xiao-Shu Jiang
- Department of Pathophysiology, Harbin Medical UniversityHarbin 150081, P. R. China
| | - Jing-Long Wang
- Pathology Center, Shanghai General Hospital/Faculty of Basic Medicine, School of Medicine, Shanghai Jiao Tong UniversityShanghai 200025, P. R. China
| | - Y Eugene Chin
- Institute of Health Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, P. R. China
| | - Guo-Hui Fu
- Pathology Center, Shanghai General Hospital/Faculty of Basic Medicine, School of Medicine, Shanghai Jiao Tong UniversityShanghai 200025, P. R. China
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Xu S, Panikker P, Iqbal S, Elefant F. Tip60 HAT Action Mediates Environmental Enrichment Induced Cognitive Restoration. PLoS One 2016; 11:e0159623. [PMID: 27454757 PMCID: PMC4959735 DOI: 10.1371/journal.pone.0159623] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/06/2016] [Indexed: 12/14/2022] Open
Abstract
Environmental enrichment (EE) conditions have beneficial effects for reinstating cognitive ability in neuropathological disorders like Alzheimer's disease (AD). While EE benefits involve epigenetic gene control mechanisms that comprise histone acetylation, the histone acetyltransferases (HATs) involved remain largely unknown. Here, we examine a role for Tip60 HAT action in mediating activity- dependent beneficial neuroadaptations to EE using the Drosophila CNS mushroom body (MB) as a well-characterized cognition model. We show that flies raised under EE conditions display enhanced MB axonal outgrowth, synaptic marker protein production, histone acetylation induction and transcriptional activation of cognition linked genes when compared to their genotypically identical siblings raised under isolated conditions. Further, these beneficial changes are impaired in both Tip60 HAT mutant flies and APP neurodegenerative flies. While EE conditions provide some beneficial neuroadaptive changes in the APP neurodegenerative fly MB, such positive changes are significantly enhanced by increasing MB Tip60 HAT levels. Our results implicate Tip60 as a critical mediator of EE-induced benefits, and provide broad insights into synergistic behavioral and epigenetic based therapeutic approaches for treatment of cognitive disorder.
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Affiliation(s)
- Songjun Xu
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Priyalakshmi Panikker
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Sahira Iqbal
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Felice Elefant
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
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Toselli-Mollereau E, Robellet X, Fauque L, Lemaire S, Schiklenk C, Klein C, Hocquet C, Legros P, N'Guyen L, Mouillard L, Chautard E, Auboeuf D, Haering CH, Bernard P. Nucleosome eviction in mitosis assists condensin loading and chromosome condensation. EMBO J 2016; 35:1565-81. [PMID: 27266525 DOI: 10.15252/embj.201592849] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 05/05/2016] [Indexed: 12/15/2022] Open
Abstract
Condensins associate with DNA and shape mitotic chromosomes. Condensins are enriched nearby highly expressed genes during mitosis, but how this binding is achieved and what features associated with transcription attract condensins remain unclear. Here, we report that condensin accumulates at or in the immediate vicinity of nucleosome-depleted regions during fission yeast mitosis. Two transcriptional coactivators, the Gcn5 histone acetyltransferase and the RSC chromatin-remodelling complex, bind to promoters adjoining condensin-binding sites and locally evict nucleosomes to facilitate condensin binding and allow efficient mitotic chromosome condensation. The function of Gcn5 is closely linked to condensin positioning, since neither the localization of topoisomerase II nor that of the cohesin loader Mis4 is altered in gcn5 mutant cells. We propose that nucleosomes act as a barrier for the initial binding of condensin and that nucleosome-depleted regions formed at highly expressed genes by transcriptional coactivators constitute access points into chromosomes where condensin binds free genomic DNA.
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Affiliation(s)
- Esther Toselli-Mollereau
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Xavier Robellet
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Lydia Fauque
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Sébastien Lemaire
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | | | - Carlo Klein
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Clémence Hocquet
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Pénélope Legros
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Lia N'Guyen
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Léo Mouillard
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Emilie Chautard
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | - Didier Auboeuf
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
| | | | - Pascal Bernard
- Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Lyon, France
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Nucleosome competition reveals processive acetylation by the SAGA HAT module. Proc Natl Acad Sci U S A 2015; 112:E5461-70. [PMID: 26401015 DOI: 10.1073/pnas.1508449112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator complex hyperacetylates histone tails in vivo in a manner that depends upon histone 3 lysine 4 trimethylation (H3K4me3), a histone mark enriched at promoters of actively transcribed genes. SAGA contains a separable subcomplex known as the histone acetyltransferase (HAT) module that contains the HAT, Gcn5, bound to Sgf29, Ada2, and Ada3. Sgf29 contains a tandem Tudor domain that recognizes H3K4me3-containing peptides and is required for histone hyperacetylation in vivo. However, the mechanism by which H3K4me3 recognition leads to lysine hyperacetylation is unknown, as in vitro studies show no effect of the H3K4me3 modification on histone peptide acetylation by Gcn5. To determine how H3K4me3 binding by Sgf29 leads to histone hyperacetylation by Gcn5, we used differential fluorescent labeling of histones to monitor acetylation of individual subpopulations of methylated and unmodified nucleosomes in a mixture. We find that the SAGA HAT module preferentially acetylates H3K4me3 nucleosomes in a mixture containing excess unmodified nucleosomes and that this effect requires the Tudor domain of Sgf29. The H3K4me3 mark promotes processive, multisite acetylation of histone H3 by Gcn5 that can account for the different acetylation patterns established by SAGA at promoters versus coding regions. Our results establish a model for Sgf29 function at gene promoters and define a mechanism governing crosstalk between histone modifications.
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Halsall JA, Turan N, Wiersma M, Turner BM. Cells adapt to the epigenomic disruption caused by histone deacetylase inhibitors through a coordinated, chromatin-mediated transcriptional response. Epigenetics Chromatin 2015; 8:29. [PMID: 26380582 PMCID: PMC4572612 DOI: 10.1186/s13072-015-0021-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/03/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The genome-wide hyperacetylation of chromatin caused by histone deacetylase inhibitors (HDACi) is surprisingly well tolerated by most eukaryotic cells. The homeostatic mechanisms that underlie this tolerance are unknown. Here we identify the transcriptional and epigenomic changes that constitute the earliest response of human lymphoblastoid cells to two HDACi, valproic acid and suberoylanilide hydroxamic acid (Vorinostat), both in widespread clinical use. RESULTS Dynamic changes in transcript levels over the first 2 h of exposure to HDACi were assayed on High Density microarrays. There was a consistent response to the two different inhibitors at several concentrations. Strikingly, components of all known lysine acetyltransferase (KAT) complexes were down-regulated, as were genes required for growth and maintenance of the lymphoid phenotype. Up-regulated gene clusters were enriched in regulators of transcription, development and phenotypic change. In untreated cells, HDACi-responsive genes, whether up- or down-regulated, were packaged in highly acetylated chromatin. This was essentially unaffected by HDACi. In contrast, HDACi induced a strong increase in H3K27me3 at transcription start sites, irrespective of their transcriptional response. Inhibition of the H3K27 methylating enzymes, EZH1/2, altered the transcriptional response to HDACi, confirming the functional significance of H3K27 methylation for specific genes. CONCLUSIONS We propose that the observed transcriptional changes constitute an inbuilt adaptive response to HDACi that promotes cell survival by minimising protein hyperacetylation, slowing growth and re-balancing patterns of gene expression. The transcriptional response to HDACi is mediated by a precisely timed increase in H3K27me3 at transcription start sites. In contrast, histone acetylation, at least at the three lysine residues tested, seems to play no direct role. Instead, it may provide a stable chromatin environment that allows transcriptional change to be induced by other factors, possibly acetylated non-histone proteins.
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Affiliation(s)
- John A Halsall
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Nil Turan
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Maaike Wiersma
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Bryan M Turner
- Chromatin and Gene Expression Group, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
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Allshire RC, Ekwall K. Epigenetic Regulation of Chromatin States in Schizosaccharomyces pombe. Cold Spring Harb Perspect Biol 2015; 7:a018770. [PMID: 26134317 DOI: 10.1101/cshperspect.a018770] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article discusses the advances made in epigenetic research using the model organism fission yeast Schizosaccharomyces pombe. S. pombe has been used for epigenetic research since the discovery of position effect variegation (PEV). This is a phenomenon in which a transgene inserted within heterochromatin is variably expressed, but can be stably inherited in subsequent cell generations. PEV occurs at centromeres, telomeres, ribosomal DNA (rDNA) loci, and mating-type regions of S. pombe chromosomes. Heterochromatin assembly in these regions requires enzymes that modify histones and the RNA interference (RNAi) machinery. One of the key histone-modifying enzymes is the lysine methyltransferase Clr4, which methylates histone H3 on lysine 9 (H3K9), a classic hallmark of heterochromatin. The kinetochore is assembled on specialized chromatin in which histone H3 is replaced by the variant CENP-A. Studies in fission yeast have contributed to our understanding of the establishment and maintenance of CENP-A chromatin and the epigenetic activation and inactivation of centromeres.
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Affiliation(s)
- Robin C Allshire
- Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Center for Biosciences, NOVUM, S-141 83, Huddinge, Sweden
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Parnell TJ, Schlichter A, Wilson BG, Cairns BR. The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism. eLife 2015; 4:e06073. [PMID: 25821983 PMCID: PMC4423118 DOI: 10.7554/elife.06073] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/28/2015] [Indexed: 12/19/2022] Open
Abstract
ISWI family chromatin remodelers typically organize nucleosome arrays, while SWI/SNF family remodelers (RSC) typically disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism and reveal different mechanisms at two different promoter architectures. DOI:http://dx.doi.org/10.7554/eLife.06073.001 The genome of an organism can contain hundreds to thousands of genes. However, these genes are not all active at the same time. Instead, mechanisms exist that control when genes are switched off or on. One such mechanism alters how tightly DNA is packaged into a structure called chromatin. To form chromatin, DNA is wrapped around histone proteins at different points along its length; these structures are known as nucleosomes. Once formed, chromatin can either adopt a tightly packed form that represses gene activity or a less compact form associated with gene activation. The proteins that control how chromatin is packed are called ‘chromatin remodelers’. These proteins work in complexes that either disassemble chromatin—for example, by repositioning nucleosomes or removing histones—or organize chromatin by replacing nucleosomes and making it more compact. Studies in many organisms have identified two key families of chromatin remodelers. In yeast, the ISWI family of complexes assembles chromatin and a protein complex called RSC disassembles chromatin. Parnell, Schlichter et al. used a range of genetic techniques to investigate whether these two chromatin-remodeling complexes work against each other in a species of yeast called Saccharomyces cerevisiae. The results suggest that this is indeed the case. Both the ISWI complex and the RSC complex bind to regions of DNA called promoters, which are found at the start of a gene and help to regulate its activity. Parnell, Schlichter et al. found that the RSC complex helps to activate genes by establishing or maintaining regions of nucleosome-poor chromatin at a promoter. The chromatin is relaxed in these regions, which allows the proteins that activate genes to access the DNA. This effect is partially counteracted by the ISWI complex, which repositions nucleosomes across the promoters to fill the gaps created by the RSC complex. In comparison, Parnell, Schlichter et al. found that promoters that do not have regions of nucleosome-poor chromatin contain a larger number of both of the remodeling complexes and have a high turnover of histone proteins. This suggests that at these sites, the RSC proteins are needed to overcome the assembly of nucleosomes by the ISWI complex in order to activate the gene. Thus, these two chromatin remodelers, ISWI and RSC, compete at promoters to determine whether they contain or lack nucleosomes, which helps determine whether the gene is silent or active, respectively. Future work will look further at how the ‘winner’ is determined: how transcription factors or signaling systems within the cell bias the recruitment or activity of RSC or ISWI at particular promoters, to determine gene activity. DOI:http://dx.doi.org/10.7554/eLife.06073.002
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Affiliation(s)
- Timothy J Parnell
- Department of Oncological Sciences, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Alisha Schlichter
- Department of Oncological Sciences, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Boris G Wilson
- Department of Oncological Sciences, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Bradley R Cairns
- Department of Oncological Sciences, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
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40
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Li T, Su L, Lei Y, Liu X, Zhang Y, Liu X. DDIT3 and KAT2A Proteins Regulate TNFRSF10A and TNFRSF10B Expression in Endoplasmic Reticulum Stress-mediated Apoptosis in Human Lung Cancer Cells. J Biol Chem 2015; 290:11108-18. [PMID: 25770212 DOI: 10.1074/jbc.m115.645333] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Indexed: 01/10/2023] Open
Abstract
TNFRSF10A and TNFRSF10B are cell surface receptors that bind to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and mediate the extrinsic pathway of apoptosis. However, the mechanisms of transcriptional regulation of TNFRSF10A and TNFRSF10B remain largely uncharacterized. In this study, two putative DDIT3 binding sites (-1636/-1625; -374/-364) and a putative AP-1 binding site (-304/-298) were identified in the TNFRSF10A promoter region. We found that DDIT3 interacts with phospho-JUN, and the DDIT3·phospho-JUN complex binds to the AP-1 binding site (-304/-298) within the TNFRSF10A promoter region. In addition, we confirmed that KAT2A physically interacts with the N-terminal region (amino acids 1-26) of DDIT3. Importantly, knockdown of KAT2A down-regulated TNFRSF10A and TNFRSF10B and dramatically decreased promoter activity of cells transfected with luciferase reporter plasmid containing the AP-1 binding site (-304/-298) of the TNFRSF10A promoter, as well as cells transfected with luciferase reporter plasmid containing DDIT3 binding site (-276/-264) of the TNFRSF10B promoter. ChIP results suggest that KAT2A may participate in a KAT2A·DDIT3·phospho-JUN complex, or may participate in a KAT2A·DDIT3 complex and acetylate H3K9/K14, respectively. Moreover, we verified that TNFRSF10A mediates apoptosis triggered by endoplasmic reticulum stress in human lung cancer cells. Collectively, we demonstrate that DDIT3 and KAT2A cooperatively up-regulate TNFRSF10A and TNFRSF10B. Our findings highlight novel mechanisms underlying endoplasmic reticulum stress-induced TNFRSF10A and TNFRSF10B expressions and apoptosis. These findings will be helpful for elucidating mechanisms related to anticancer drugs in mediating apoptosis.
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Affiliation(s)
- Tianliang Li
- From the Shandong University School of Life Sciences, Jinan 250100, China
| | - Ling Su
- From the Shandong University School of Life Sciences, Jinan 250100, China
| | - Yuanjiu Lei
- From the Shandong University School of Life Sciences, Jinan 250100, China
| | - Xianfang Liu
- From the Shandong University School of Life Sciences, Jinan 250100, China
| | - Yajing Zhang
- From the Shandong University School of Life Sciences, Jinan 250100, China
| | - Xiangguo Liu
- From the Shandong University School of Life Sciences, Jinan 250100, China
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41
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Abstract
Transcription elongation by RNA polymerase II (RNAP II) involves the coordinated action of numerous regulatory factors. Among these are chromatin-modifying enzymes, which generate a stereotypic and conserved pattern of histone modifications along transcribed genes. This pattern implies a precise coordination between regulators of histone modification and the RNAP II elongation complex. Here I review the pathways and molecular events that regulate co-transcriptional histone modifications. Insight into these events will illuminate the assembly of functional RNAP II elongation complexes and how the chromatin landscape influences their composition and function.
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Affiliation(s)
- Jason C Tanny
- a Department of Pharmacology and Therapeutics ; McGill University ; Montreal , Canada
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42
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Bonnet J, Wang CY, Baptista T, Vincent SD, Hsiao WC, Stierle M, Kao CF, Tora L, Devys D. The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription. Genes Dev 2014; 28:1999-2012. [PMID: 25228644 PMCID: PMC4173158 DOI: 10.1101/gad.250225.114] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The SAGA coactivator complex contains distinct chromatin-modifying activities and is recruited by DNA-bound activators to regulate the expression of a subset of genes. Bonnet et al. discovered that SAGA acetylates the promoters and deubiquitinates the transcribed region of all expressed genes. SAGA also plays a critical role for RNA polymerase II recruitment at all expressed genes. This study uncovers a new function for SAGA as a bona fide cofactor for all RNA polymerase II transcription. The SAGA (Spt–Ada–Gcn5 acetyltransferase) coactivator complex contains distinct chromatin-modifying activities and is recruited by DNA-bound activators to regulate the expression of a subset of genes. Surprisingly, recent studies revealed little overlap between genome-wide SAGA-binding profiles and changes in gene expression upon depletion of subunits of the complex. As indicators of SAGA recruitment on chromatin, we monitored in yeast and human cells the genome-wide distribution of histone H3K9 acetylation and H2B ubiquitination, which are respectively deposited or removed by SAGA. Changes in these modifications after inactivation of the corresponding enzyme revealed that SAGA acetylates the promoters and deubiquitinates the transcribed region of all expressed genes. In agreement with this broad distribution, we show that SAGA plays a critical role for RNA polymerase II recruitment at all expressed genes. In addition, through quantification of newly synthesized RNA, we demonstrated that SAGA inactivation induced a strong decrease of mRNA synthesis at all tested genes. Analysis of the SAGA deubiquitination activity further revealed that SAGA acts on the whole transcribed genome in a very fast manner, indicating a highly dynamic association of the complex with chromatin. Thus, our study uncovers a new function for SAGA as a bone fide cofactor for all RNA polymerase II transcription.
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Affiliation(s)
- Jacques Bonnet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France; U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, Cedex, France
| | - Chen-Yi Wang
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Tiago Baptista
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France; U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, Cedex, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France; U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, Cedex, France
| | - Wei-Chun Hsiao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Matthieu Stierle
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France; U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, Cedex, France
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France; U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, Cedex, France
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; UMR7104, Centre National de la Recherche Scientifique, 67404 Illkirch, France; U964, Institut National de la Santé et de la Recherche Médicale, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, Cedex, France;
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43
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Gcn5 and PCAF regulate PPARγ and Prdm16 expression to facilitate brown adipogenesis. Mol Cell Biol 2014; 34:3746-53. [PMID: 25071153 DOI: 10.1128/mcb.00622-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The acetyltransferase Gcn5 is critical for embryogenesis and shows partial functional redundancy with its homolog PCAF. However, the tissue- and cell lineage-specific functions of Gcn5 and PCAF are still not well defined. Here we probe the functions of Gcn5 and PCAF in adipogenesis. We found that the double knockout (DKO) of Gcn5/PCAF inhibits expression of the master adipogenic transcription factor gene PPARγ, thereby preventing adipocyte differentiation. The adipogenesis defects in Gcn5/PCAF DKO cells are rescued by ectopic expression of peroxisome proliferator-activated receptor γ (PPARγ), suggesting Gcn5/PCAF act upstream of PPARγ to facilitate adipogenesis. The requirement of Gcn5/PCAF for PPARγ expression was unexpectedly bypassed by prolonged treatment with an adipogenic inducer, 3-isobutyl-1-methylxanthine (IBMX). However, neither PPARγ ectopic expression nor prolonged IBMX treatment rescued defects in Prdm16 expression in DKO cells, indicating that Gcn5/PCAF are essential for normal Prdm16 expression. Gcn5/PCAF regulate PPARγ and Prdm16 expression at different steps in the transcription process, facilitating RNA polymerase II recruitment to Prdm16 and elongation of PPARγ transcripts. Overall, our study reveals that Gcn5/PCAF facilitate adipogenesis through regulation of PPARγ expression and regulate brown adipogenesis by influencing Prdm16 expression.
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44
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Stilling RM, Rönicke R, Benito E, Urbanke H, Capece V, Burkhardt S, Bahari-Javan S, Barth J, Sananbenesi F, Schütz AL, Dyczkowski J, Martinez-Hernandez A, Kerimoglu C, Dent SYR, Bonn S, Reymann KG, Fischer A. K-Lysine acetyltransferase 2a regulates a hippocampal gene expression network linked to memory formation. EMBO J 2014; 33:1912-27. [PMID: 25024434 DOI: 10.15252/embj.201487870] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Neuronal histone acetylation has been linked to memory consolidation, and targeting histone acetylation has emerged as a promising therapeutic strategy for neuropsychiatric diseases. However, the role of histone-modifying enzymes in the adult brain is still far from being understood. Here we use RNA sequencing to screen the levels of all known histone acetyltransferases (HATs) in the hippocampal CA1 region and find that K-acetyltransferase 2a (Kat2a)--a HAT that has not been studied for its role in memory function so far--shows highest expression. Mice that lack Kat2a show impaired hippocampal synaptic plasticity and long-term memory consolidation. We furthermore show that Kat2a regulates a highly interconnected hippocampal gene expression network linked to neuroactive receptor signaling via a mechanism that involves nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). In conclusion, our data establish Kat2a as a novel and essential regulator of hippocampal memory consolidation.
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Affiliation(s)
- Roman M Stilling
- Department of Psychiatry and Psychotherapy, University Medical Center, Göttingen, Germany
| | - Raik Rönicke
- Research group for Pathophysiology in Dementia, German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Eva Benito
- Research group for Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Hendrik Urbanke
- Research group for Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Vincenzo Capece
- Research group for Computational Analysis of Biological Networks, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Susanne Burkhardt
- Research group for Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Sanaz Bahari-Javan
- Research group for Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Jonas Barth
- Research group for Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Farahnaz Sananbenesi
- Department of Psychiatry and Psychotherapy, University Medical Center, Göttingen, Germany
| | - Anna L Schütz
- Research group for Computational Analysis of Biological Networks, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Jerzy Dyczkowski
- Research group for Computational Analysis of Biological Networks, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Ana Martinez-Hernandez
- Research group for Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Cemil Kerimoglu
- Department of Psychiatry and Psychotherapy, University Medical Center, Göttingen, Germany
| | - Sharon Y R Dent
- MD Anderson Cancer Center, University of Texas, Smithville, TX, USA
| | - Stefan Bonn
- Research group for Computational Analysis of Biological Networks, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Klaus G Reymann
- Research group for Pathophysiology in Dementia, German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Andre Fischer
- Department of Psychiatry and Psychotherapy, University Medical Center, Göttingen, Germany Research group for Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
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45
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Legionella pneumophila type IV effectors hijack the transcription and translation machinery of the host cell. Trends Cell Biol 2014; 24:771-8. [PMID: 25012125 DOI: 10.1016/j.tcb.2014.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 01/26/2023]
Abstract
Intracellular bacterial pathogens modulate the host response to persist and replicate inside a eukaryotic cell and cause disease. Legionella pneumophila, the causative agent of Legionnaires' disease, is present in freshwater environments and represents one of these pathogens. During coevolution with protozoan cells, L. pneumophila has acquired highly sophisticated and diverse strategies to hijack host cell processes. It secretes hundreds of effectors into the host cell, and these manipulate host signaling pathways and key cellular processes. Recently it has been shown that L. pneumophila is also able to alter the transcription and translation machinery of the host and to exploit epigenetic mechanisms in the cells it resides in to counteract host responses.
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46
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The histone acetyltransferase MOF activates hypothalamic polysialylation to prevent diet-induced obesity in mice. Mol Metab 2014; 3:619-29. [PMID: 25161885 PMCID: PMC4142401 DOI: 10.1016/j.molmet.2014.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 12/11/2022] Open
Abstract
Overfeeding causes rapid synaptic remodeling in hypothalamus feeding circuits. Polysialylation of cell surface molecules is a key step in this neuronal rewiring and allows normalization of food intake. Here we examined the role of hypothalamic polysialylation in the long-term maintenance of body weight, and deciphered the molecular sequence underlying its nutritional regulation. We found that upon high fat diet (HFD), reduced hypothalamic polysialylation exacerbated the diet-induced obese phenotype in mice. Upon HFD, the histone acetyltransferase MOF was rapidly recruited on the St8sia4 polysialyltransferase-encoding gene. Mof silencing in the mediobasal hypothalamus of adult mice prevented activation of the St8sia4 gene transcription, reduced polysialylation, altered the acute homeostatic feeding response to HFD and increased the body weight gain. These findings indicate that impaired hypothalamic polysialylation contribute to the development of obesity, and establish a role for MOF in the brain control of energy balance.
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47
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Suter MA, Ma J, Vuguin PM, Hartil K, Fiallo A, Harris RA, Charron MJ, Aagaard KM. In utero exposure to a maternal high-fat diet alters the epigenetic histone code in a murine model. Am J Obstet Gynecol 2014; 210:463.e1-463.e11. [PMID: 24793723 DOI: 10.1016/j.ajog.2014.01.045] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/14/2014] [Accepted: 01/31/2014] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Data from animal models show that in utero exposure to a maternal high-fat diet (HFD) renders susceptibility of these offspring to the adult onset of metabolic syndrome. We and others have previously shown that epigenetic modifications to histones may serve as a molecular memory of the in utero exposure, rendering the risk of adult disease. Because mice heterozygous for the Glut4 gene (insulin sensitive glucose transporter) born to wild-type (WT) mothers demonstrate exacterbated metabolic syndrome when exposed to an HFD in utero, we sought to analyze the genome-wide epigenetic changes that occur in the fetal liver in susceptible offspring. STUDY DESIGN WT and Glut4(+/-) (G4(+/-)) offspring of WT mothers that were exposed either to a control or an HFD in utero were studied. Immunoblotting was used to measure hepatic histone modifications of fetal and 5-week animals. Chromatin immunoprecipitation (ChIP) followed by hybridization to chip arrays (ChIP-on-chip) was used to detect genome-wide changes of histone modifications with HFD exposure. RESULTS We found that levels of hepatic H3K14ac and H3K9me3 significantly increased with HFD exposure in WT and G4(+/-) fetal and 5-week offspring. Pathway analysis of our ChIP-on-chip data revealed differential H3K14ac and H3K9me3 enrichment along pathways that regulate lipid metabolism, specifically in the promoter regions of Pparg, Ppara, Rxra, and Rora. CONCLUSION We conclude that HFD exposure in utero is associated with functional alterations to fetal hepatic histone modifications in both WT and G4(+/-) offspring, some of which persist up to 5 weeks of age.
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Affiliation(s)
- Melissa A Suter
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | - Jun Ma
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | - Patricia M Vuguin
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY; Division of Pediatric Endocrinology, Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY
| | - Kirsten Hartil
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY
| | - Ariana Fiallo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY
| | - R Alan Harris
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | - Maureen J Charron
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY; Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY
| | - Kjersti M Aagaard
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX.
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Magraner-Pardo L, Pelechano V, Coloma MD, Tordera V. Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae. BMC Genomics 2014; 15:247. [PMID: 24678875 PMCID: PMC3986647 DOI: 10.1186/1471-2164-15-247] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 03/24/2014] [Indexed: 12/17/2022] Open
Abstract
Background Specific histone modifications play important roles in chromatin functions; i.e., activation or repression of gene transcription. This participation must occur as a dynamic process. Nevertheless, most of the histone modification maps reported to date provide only static pictures that link certain modifications with active or silenced states. This study, however, focuses on the global histone modification variation that occurs in response to the transcriptional reprogramming produced by a physiological perturbation in yeast. Results We did a genome-wide chromatin immunoprecipitation analysis for eight specific histone modifications before and after saline stress. The most striking change was rapid acetylation loss in lysines 9 and 14 of H3 and in lysine 8 of H4, associated with gene repression. The genes activated by saline stress increased the acetylation levels at these same sites, but this acetylation process was quantitatively minor if compared to that of the deacetylation of repressed genes. The changes in the tri-methylation of lysines 4, 36 and 79 of H3 and the di-methylation of lysine 79 of H3 were slighter than those of acetylation. Furthermore, we produced new genome-wide maps for seven histone modifications, and we analyzed, for the first time in S. cerevisiae, the genome-wide profile of acetylation of lysine 8 of H4. Conclusions This research reveals that the short-term changes observed in the post-stress methylation of histones are much more moderate than those of acetylation, and that the dynamics of the acetylation state of histones during activation or repression of transcription is a much quicker process than methylation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-247) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Vicente Tordera
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr, Moliner 50, 46100 Burjassot, València, Spain.
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Wang J, Dixon SE, Ting LM, Liu TK, Jeffers V, Croken MM, Calloway M, Cannella D, Ali Hakimi M, Kim K, Sullivan WJ. Lysine acetyltransferase GCN5b interacts with AP2 factors and is required for Toxoplasma gondii proliferation. PLoS Pathog 2014; 10:e1003830. [PMID: 24391497 PMCID: PMC3879359 DOI: 10.1371/journal.ppat.1003830] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/26/2013] [Indexed: 12/26/2022] Open
Abstract
Histone acetylation has been linked to developmental changes in gene expression and is a validated drug target of apicomplexan parasites, but little is known about the roles of individual histone modifying enzymes and how they are recruited to target genes. The protozoan parasite Toxoplasma gondii (phylum Apicomplexa) is unusual among invertebrates in possessing two GCN5-family lysine acetyltransferases (KATs). While GCN5a is required for gene expression in response to alkaline stress, this KAT is dispensable for parasite proliferation in normal culture conditions. In contrast, GCN5b cannot be disrupted, suggesting it is essential for Toxoplasma viability. To further explore the function of GCN5b, we generated clonal parasites expressing an inducible HA-tagged dominant-negative form of GCN5b containing a point mutation that ablates enzymatic activity (E703G). Stabilization of this dominant-negative GCN5b was mediated through ligand-binding to a destabilization domain (dd) fused to the protein. Induced accumulation of the ddHAGCN5b(E703G) protein led to a rapid arrest in parasite replication. Growth arrest was accompanied by a decrease in histone H3 acetylation at specific lysine residues as well as reduced expression of GCN5b target genes in GCN5b(E703G) parasites, which were identified using chromatin immunoprecipitation coupled with microarray hybridization (ChIP-chip). Proteomics studies revealed that GCN5b interacts with AP2-domain proteins, apicomplexan plant-like transcription factors, as well as a “core complex” that includes the co-activator ADA2-A, TFIID subunits, LEO1 polymerase-associated factor (Paf1) subunit, and RRM proteins. The dominant-negative phenotype of ddHAGCN5b(E703G) parasites, considered with the proteomics and ChIP-chip data, indicate that GCN5b plays a central role in transcriptional and chromatin remodeling complexes. We conclude that GCN5b has a non-redundant and indispensable role in regulating gene expression required during the Toxoplasma lytic cycle. Toxoplasma gondii is a protozoan parasite that causes significant opportunistic infection in AIDS and other immunocompromised patients. Acute episodes of toxoplasmosis stem from tissue destruction caused by the rapidly growing form of the parasite, the tachyzoite. In this study, we identify a lysine acetyltransferase (KAT) enzyme called GCN5b that is an essential driver of tachyzoite proliferation. Our studies show that GCN5b is present at a wide variety of parasite genes and that expression of defective GCN5b compromises gene expression through its diminished ability to acetylate histone proteins. We also identified the likely mechanism by which GCN5b is recruited to target genes by co-purifying this KAT with plant-like AP2-domain proteins, a subset of which function as DNA-binding transcription factors in Apicomplexa. Our findings demonstrate that KATs play a critical role in parasite replication, which leads to tissue destruction and acute disease in the host. Parasite KAT enzyme complexes may therefore serve as attractive targets for future drug development.
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Affiliation(s)
- Jiachen Wang
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Stacy E. Dixon
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Li-Min Ting
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Ting-Kai Liu
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Victoria Jeffers
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Matthew M. Croken
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Myrasol Calloway
- Laboratory for Macromolecular Analysis, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | | | | | - Kami Kim
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - William J. Sullivan
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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50
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Forbes NE, Abdelbary H, Lupien M, Bell JC, Diallo JS. Exploiting tumor epigenetics to improve oncolytic virotherapy. Front Genet 2013; 4:184. [PMID: 24062768 PMCID: PMC3778850 DOI: 10.3389/fgene.2013.00184] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 08/29/2013] [Indexed: 12/20/2022] Open
Abstract
Oncolytic viruses (OVs) comprise a versatile and multi-mechanistic therapeutic platform in the growing arsenal of anticancer biologics. These replicating therapeutics find favorable conditions in the tumor niche, characterized among others by increased metabolism, reduced anti-tumor/antiviral immunity, and disorganized vasculature. Through a self-amplification that is dependent on multiple cancer-specific defects, these agents exhibit remarkable tumor selectivity. With several OVs completing or entering Phase III clinical evaluation, their therapeutic potential as well as the challenges ahead are increasingly clear. One key hurdle is tumor heterogeneity, which results in variations in the ability of tumors to support productive infection by OVs and to induce adaptive anti-tumor immunity. To this end, mounting evidence suggests tumor epigenetics may play a key role. This review will focus on the epigenetic landscape of tumors and how it relates to OV infection. Therapeutic strategies aiming to exploit the epigenetic identity of tumors in order to improve OV therapy are also discussed.
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Affiliation(s)
- Nicole E. Forbes
- Center for Innovative Cancer Research, Ottawa Hospital Research InstituteOttawa, ON, Canada
- Faculty of Medicine, University of OttawaOttawa, ON, Canada
| | - Hesham Abdelbary
- Center for Innovative Cancer Research, Ottawa Hospital Research InstituteOttawa, ON, Canada
- Faculty of Medicine, University of OttawaOttawa, ON, Canada
| | - Mathieu Lupien
- Ontario Cancer Institute, Princess Margaret Cancer Center/University Health NetworkToronto, ON, Canada
- Ontario Institute for Cancer ResearchToronto, ON, Canada
- Department of Medical Biophysics, University of TorontoToronto, ON, Canada
| | - John C. Bell
- Center for Innovative Cancer Research, Ottawa Hospital Research InstituteOttawa, ON, Canada
- Faculty of Medicine, University of OttawaOttawa, ON, Canada
| | - Jean-Simon Diallo
- Center for Innovative Cancer Research, Ottawa Hospital Research InstituteOttawa, ON, Canada
- Faculty of Medicine, University of OttawaOttawa, ON, Canada
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