101
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Wang X, Moazed D. DNA sequence-dependent epigenetic inheritance of gene silencing and histone H3K9 methylation. Science 2017; 356:88-91. [PMID: 28302794 DOI: 10.1126/science.aaj2114] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 02/13/2017] [Indexed: 12/30/2022]
Abstract
Epigenetic inheritance mechanisms play fundamental roles in maintaining cellular memory of gene expression states. In fission yeast, histone H3 lysine 9 (H3K9) is methylated (H3K9me) at heterochromatic domains. These domains can be epigenetically inherited when epe1+ , encoding an enzyme that promotes H3K9 demethylation, is deleted. How native epigenetic states are stably maintained in epe1+ cells remains unknown. Here, we developed a system to examine the role of DNA sequence and genomic context in propagation of a cis-heritable H3K9me-dependent silenced state. We show that in epe1+ cells, in addition to sequence-independent mechanisms that propagate H3K9me, epigenetic inheritance of silencing requires binding sites for sequence-dependent activating transcription factor (ATF)-adenosine 3',5'-monophosphate (cAMP) response element-binding protein (CREB) family transcription factors within their native chromosomal context. Thus, specific DNA sequences contribute to cis inheritance of H3K9me and silent epigenetic states.
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Affiliation(s)
- Xiaoyi Wang
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Danesh Moazed
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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102
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Boycheva I, Vassileva V, Revalska M, Zehirov G, Iantcheva A. Different functions of the histone acetyltransferase HAC1 gene traced in the model species Medicago truncatula, Lotus japonicus and Arabidopsis thaliana. PROTOPLASMA 2017; 254:697-711. [PMID: 27180194 DOI: 10.1007/s00709-016-0983-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 05/06/2016] [Indexed: 05/26/2023]
Abstract
In eukaryotes, histone acetyltransferases regulate the acetylation of histones and transcription factors, affecting chromatin structural organization, transcriptional regulation, and gene activation. To assess the role of HAC1, a gene encoding for a histone acetyltransferase in Medicago truncatula, stable transgenic lines with modified HAC1 expression in the model plants M. truncatula, Lotus japonicus, and Arabidopsis thaliana were generated by Agrobacterium-mediated transformation and used for functional analyses. Histochemical, transcriptional, flow cytometric, and morphological analyses demonstrated the involvement of HAC1 in plant growth and development, responses to internal stimuli, and cell cycle progression. Expression patterns of a reporter gene encoding beta-glucuronidase (GUS) fused to the HAC1 promoter sequence were associated with young tissues comprised of actively dividing cells in different plant organs. The green fluorescent protein (GFP) signal, driven by the HAC1 promoter, was detected in the nuclei and cytoplasm of root cells. Transgenic lines with HAC1 overexpression and knockdown showed a wide range of phenotypic deviations and developmental abnormalities, which provided lines of evidence for the role of HAC1 in plant development. Synchronization of A. thaliana root tips in a line with HAC1 knockdown showed the involvement of this gene in the acetylation of two core histones during S phase of the plant cell cycle.
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Affiliation(s)
- Irina Boycheva
- AgroBioInstitute, Blvd. Dragan Tzankov 8, 1164, Sofia, Bulgaria
| | - Valya Vassileva
- Institute of Plant Physiology and Genetics, Acad. Georgi Bonchev Str., Bl. 21, 1113, Sofia, Bulgaria
| | | | - Grigor Zehirov
- Institute of Plant Physiology and Genetics, Acad. Georgi Bonchev Str., Bl. 21, 1113, Sofia, Bulgaria
| | - Anelia Iantcheva
- AgroBioInstitute, Blvd. Dragan Tzankov 8, 1164, Sofia, Bulgaria.
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103
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Fina JP, Masotti F, Rius SP, Crevacuore F, Casati P. HAC1 and HAF1 Histone Acetyltransferases Have Different Roles in UV-B Responses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:1179. [PMID: 28740501 PMCID: PMC5502275 DOI: 10.3389/fpls.2017.01179] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/20/2017] [Indexed: 05/17/2023]
Abstract
Arabidopsis has 12 histone acetyltransferases grouped in four families: the GNAT/HAG, the MYST/HAM, the p300/CBP/HAC and the TAFII250/HAF families. We previously showed that ham1 and ham2 mutants accumulated higher damaged DNA after UV-B exposure than WT plants. In contrast, hag3 RNA interference transgenic plants showed less DNA damage and lower inhibition of plant growth by UV-B, and increased levels of UV-B-absorbing compounds. These results demonstrated that HAM1, HAM2, and HAG3 participate in UV-B-induced DNA damage repair and signaling. In this work, to further explore the role of histone acetylation in UV-B responses, a putative function of other acetyltransferases of the HAC and the HAF families was analyzed. Neither HAC nor HAF acetyltrasferases participate in DNA damage and repair after UV-B radiation in Arabidopsis. Despite this, haf1 mutants presented lower inhibition of leaf and root growth by UV-B, with altered expression of E2F transcription factors. On the other hand, hac1 plants showed a delay in flowering time after UV-B exposure and changes in FLC and SOC1 expression patterns. Our data indicate that HAC1 and HAF1 have crucial roles for in UV-B signaling, confirming that, directly or indirectly, both enzymes also have a role in UV-B responses.
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104
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Chwialkowska K, Korotko U, Kosinska J, Szarejko I, Kwasniewski M. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes. FRONTIERS IN PLANT SCIENCE 2017; 8:2056. [PMID: 29250096 PMCID: PMC5714927 DOI: 10.3389/fpls.2017.02056] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/16/2017] [Indexed: 05/14/2023]
Abstract
Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop plants with large and complex genomes.
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Affiliation(s)
- Karolina Chwialkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Urszula Korotko
- Department of Genetics, University of Silesia in Katowice, Katowice, Poland
| | - Joanna Kosinska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Szarejko
- Department of Genetics, University of Silesia in Katowice, Katowice, Poland
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
- *Correspondence: Miroslaw Kwasniewski
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105
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NEMATPOUR F, MAHBOUDI F, KHALAJ V, VAZIRI B, AHMADI S, AHMADI M, EBADAT S, DAVAMI F. Optimization of monoclonal antibody expression in CHOcells by employing epigenetic gene regulation tools. Turk J Biol 2017. [DOI: 10.3906/biy-1702-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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106
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Tung SY, Wang SH, Lee SP, Tsai SP, Shen HH, Chen FJ, Wu YY, Hsiao SP, Liou GG. Modulations of SIR-nucleosome interactions of reconstructed yeast silent pre-heterochromatin by O-acetyl-ADP-ribose and magnesium. Mol Biol Cell 2016; 28:381-386. [PMID: 27932495 PMCID: PMC5341722 DOI: 10.1091/mbc.e16-06-0359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 11/22/2016] [Accepted: 11/29/2016] [Indexed: 12/25/2022] Open
Abstract
In vitro–assembled filaments are confirmed as SIR-nucleosome pre-heterochromatin, and AAR acts as a modulator for their formation. Not only is magnesium present in the environmental buffer, but it also is chelated by the SIR-nucleosome pre-heterochromatin to promote its condensation. Yeast silent heterochromatin provides an excellent model with which to study epigenetic inheritance. Previously we developed an in vitro assembly system to demonstrate the formation of filament structures with requirements that mirror yeast epigenetic gene silencing in vivo. However, the properties of these filaments were not investigated in detail. Here we show that the assembly system requires Sir2, Sir3, Sir4, nucleosomes, and O-acetyl-ADP-ribose. We also demonstrate that all Sir proteins and nucleosomes are components of these filaments to prove that they are SIR-nucleosome filaments. Furthermore, we show that the individual localization patterns of Sir proteins on the SIR-nucleosome filament reflect those patterns on telomeres in vivo. In addition, we reveal that magnesium exists in the SIR-nucleosome filament, with a role similar to that for chromatin condensation. These results suggest that a small number of proteins and molecules are sufficient to mediate the formation of a minimal yeast silent pre-heterochromatin in vitro.
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Affiliation(s)
- Shu-Yun Tung
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Sue-Hong Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung 402, Taiwan
| | - Sue-Ping Lee
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Shu-Ping Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Hsiao-Hsuian Shen
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan
| | - Feng-Jung Chen
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan
| | - Yu-Yi Wu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan
| | - Sheng-Pin Hsiao
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan
| | - Gunn-Guang Liou
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan .,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan.,Guang EM Laboratory, New Taipei 242, Taiwan
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107
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Villota-Salazar NA, Mendoza-Mendoza A, González-Prieto JM. Epigenetics: from the past to the present. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1249033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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108
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Behrouzi R, Lu C, Currie MA, Jih G, Iglesias N, Moazed D. Heterochromatin assembly by interrupted Sir3 bridges across neighboring nucleosomes. eLife 2016; 5. [PMID: 27835568 PMCID: PMC5106214 DOI: 10.7554/elife.17556] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 10/18/2016] [Indexed: 01/05/2023] Open
Abstract
Heterochromatin is a conserved feature of eukaryotic chromosomes with central roles in regulation of gene expression and maintenance of genome stability. Heterochromatin formation involves spreading of chromatin-modifying factors away from initiation points over large DNA domains by poorly understood mechanisms. In Saccharomyces cerevisiae, heterochromatin formation requires the SIR complex, which contains subunits with histone-modifying, histone-binding, and self-association activities. Here, we analyze binding of the Sir proteins to reconstituted mono-, di-, tri-, and tetra-nucleosomal chromatin templates and show that key Sir-Sir interactions bridge only sites on different nucleosomes but not sites on the same nucleosome, and are therefore 'interrupted' with respect to sites on the same nucleosome. We observe maximal binding affinity and cooperativity to unmodified di-nucleosomes and propose that nucleosome pairs bearing unmodified histone H4-lysine16 and H3-lysine79 form the fundamental units of Sir chromatin binding and that cooperative binding requiring two appropriately modified nucleosomes mediates selective Sir recruitment and spreading.
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Affiliation(s)
- Reza Behrouzi
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Chenning Lu
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Mark A Currie
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Gloria Jih
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Nahid Iglesias
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Danesh Moazed
- Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
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109
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Abstract
Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effect on growth and crop yield. Details are fast emerging on the genetic/molecular regulators, at whole-genome levels, of plant responses to mineral deficiencies in model and crop plants. These genetic regulators determine the root architecture and physiological adaptations for better uptake and utilization of minerals from soil. Recent evidence also shows the potential roles of epigenetic mechanisms in gene regulation, driven by minerals imbalance. Mineral deficiency or sufficiency leads to developmental plasticity in plants for adaptation, which is preceded by a change in the pattern of gene expression. Notably, such changes at molecular levels are also influenced by altered chromatin structure and methylation patterns, or involvement of other epigenetic components. Interestingly, many of the changes induced by mineral deficiency are also inheritable in the form of epigenetic memory. Unravelling these mechanisms in response to mineral deficiency would further advance our understanding of this complex plant response. Further studies on such approaches may serve as an exciting interaction model of epigenetic and genetic regulations of mineral homeostasis in plants and designing strategies for crop improvement.
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110
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Heterologous expression of the Streptococcus pneumoniae yoeB and pezT toxin genes is lethal in Chlorella vulgaris. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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111
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Gao R, Wang H, Dong B, Yang X, Chen S, Jiang J, Zhang Z, Liu C, Zhao N, Chen F. Morphological, Genome and Gene Expression Changes in Newly Induced Autopolyploid Chrysanthemum lavandulifolium (Fisch. ex Trautv.) Makino. Int J Mol Sci 2016; 17:E1690. [PMID: 27735845 PMCID: PMC5085722 DOI: 10.3390/ijms17101690] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 12/13/2022] Open
Abstract
Autopolyploidy is widespread in higher plants and plays an important role in the process of evolution. The present study successfully induced autotetraploidys from Chrysanthemum lavandulifolium by colchicine. The plant morphology, genomic, transcriptomic, and epigenetic changes between tetraploid and diploid plants were investigated. Ligulate flower, tubular flower and leaves of tetraploid plants were greater than those of the diploid plants. Compared with diploid plants, the genome changed as a consequence of polyploidization in tetraploid plants, namely, 1.1% lost fragments and 1.6% novel fragments occurred. In addition, DNA methylation increased after genome doubling in tetraploid plants. Among 485 common transcript-derived fragments (TDFs), which existed in tetraploid and diploid progenitors, 62 fragments were detected as differentially expressed TDFs, 6.8% of TDFs exhibited up-regulated gene expression in the tetraploid plants and 6.0% exhibited down-regulation. The present study provides a reference for further studying the autopolyploidization role in the evolution of C. lavandulifolium. In conclusion, the autopolyploid C. lavandulifolium showed a global change in morphology, genome and gene expression compared with corresponding diploid.
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Affiliation(s)
- Ri Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
- Department of Horticulture, Agricultural College Yanbian University, Park Road 977, Yanji 133002, China.
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Bin Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiaodong Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhaohe Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chen Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Nan Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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112
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Desiderio A, Spinelli R, Ciccarelli M, Nigro C, Miele C, Beguinot F, Raciti GA. Epigenetics: spotlight on type 2 diabetes and obesity. J Endocrinol Invest 2016; 39:1095-103. [PMID: 27180180 DOI: 10.1007/s40618-016-0473-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/18/2016] [Indexed: 12/15/2022]
Abstract
Type 2 diabetes (T2D) and obesity are the major public health problems. Substantial efforts have been made to define loci and variants contributing to the individual risk of these disorders. However, the overall risk explained by genetic variation is very modest. Epigenetics is one of the fastest growing research areas in biomedicine as changes in the epigenome are involved in many biological processes, impact on the risk for several complex diseases including diabetes and may explain susceptibility. In this review, we focus on the role of DNA methylation in contributing to the risk of T2D and obesity.
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Affiliation(s)
- A Desiderio
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, Italy
- Department of Translational Medical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
| | - R Spinelli
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, Italy
- Department of Translational Medical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
| | - M Ciccarelli
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, Italy
- Department of Translational Medical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
| | - C Nigro
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, Italy
- Department of Translational Medical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
| | - C Miele
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, Italy
- Department of Translational Medical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
| | - F Beguinot
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, Italy.
- Department of Translational Medical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy.
| | - G A Raciti
- URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Council of Research, Naples, Italy
- Department of Translational Medical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
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113
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Loss of Tau protein affects the structure, transcription and repair of neuronal pericentromeric heterochromatin. Sci Rep 2016; 6:33047. [PMID: 27605042 PMCID: PMC5015075 DOI: 10.1038/srep33047] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/04/2016] [Indexed: 12/27/2022] Open
Abstract
Pericentromeric heterochromatin (PCH) gives rise to highly dense chromatin sub-structures rich in the epigenetic mark corresponding to the trimethylated form of lysine 9 of histone H3 (H3K9me3) and in heterochromatin protein 1α (HP1α), which regulate genome expression and stability. We demonstrate that Tau, a protein involved in a number of neurodegenerative diseases including Alzheimer's disease (AD), binds to and localizes within or next to neuronal PCH in primary neuronal cultures from wild-type mice. Concomitantly, we show that the clustered distribution of H3K9me3 and HP1α, two hallmarks of PCH, is disrupted in neurons from Tau-deficient mice (KOTau). Such altered distribution of H3K9me3 that could be rescued by overexpressing nuclear Tau protein was also observed in neurons from AD brains. Moreover, the expression of PCH non-coding RNAs, involved in PCH organization, was disrupted in KOTau neurons that displayed an abnormal accumulation of stress-induced PCH DNA breaks. Altogether, our results demonstrate a new physiological function of Tau in directly regulating neuronal PCH integrity that appears disrupted in AD neurons.
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114
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The Impact of External Factors on the Epigenome: In Utero and over Lifetime. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2568635. [PMID: 27294112 PMCID: PMC4887632 DOI: 10.1155/2016/2568635] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/12/2016] [Accepted: 04/26/2016] [Indexed: 01/07/2023]
Abstract
Epigenetic marks change during fetal development, adult life, and aging. Some changes play an important role in the establishment and regulation of gene programs, but others seem to occur without any apparent physiological role. An important future challenge in the field of epigenetics will be to describe how the environment affects both of these types of epigenetic change and to learn if interaction between them can determine healthy and disease phenotypes during lifetime. Here we discuss how chemical and physical environmental stressors, diet, life habits, and pharmacological treatments can affect the epigenome during lifetime and the possible impact of these epigenetic changes on pathophysiological processes.
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115
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Schimka S, Santer S, Mujkić-Ninnemann NM, Bléger D, Hartmann L, Wehle M, Lipowsky R, Santer M. Photosensitive Peptidomimetic for Light-Controlled, Reversible DNA Compaction. Biomacromolecules 2016; 17:1959-68. [DOI: 10.1021/acs.biomac.6b00052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Selina Schimka
- Institute
of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
- Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Svetlana Santer
- Institute
of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
| | | | - David Bléger
- Humboldt-Universität
zu Berlin, 12489 Berlin, Germany
| | - Laura Hartmann
- Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Marko Wehle
- Theory
and Bio-Systems Group, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Reinhard Lipowsky
- Theory
and Bio-Systems Group, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Mark Santer
- Theory
and Bio-Systems Group, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
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116
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Pérez-Campo FM, Riancho JA. Epigenetic Mechanisms Regulating Mesenchymal Stem Cell Differentiation. Curr Genomics 2016; 16:368-83. [PMID: 27019612 PMCID: PMC4765524 DOI: 10.2174/1389202916666150817202559] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 03/27/2015] [Accepted: 04/07/2015] [Indexed: 12/28/2022] Open
Abstract
Human Mesenchymal Stem Cells (hMSCs) have emerged in the last few years as one of the most promising therapeutic cell sources and, in particular, as an important tool for regenerative medicine of skeletal tissues. Although they present a more restricted potency than Embryonic Stem (ES) cells, the use of hMCS in regenerative medicine avoids many of the drawbacks characteristic of ES cells or induced pluripotent stem cells. The challenge in using these cells lies into developing precise protocols for directing cellular differentiation to generate a specific cell lineage. In order to achieve this goal, it is of the upmost importance to be able to control de process of fate decision and lineage commitment. This process requires the coordinate regulation of different molecular layers at transcriptional, posttranscriptional and translational levels. At the transcriptional level, switching on and off different sets of genes is achieved not only through transcriptional regulators, but also through their interplay with epigenetic modifiers. It is now well known that epigenetic changes take place in an orderly way through development and are critical in the determination of lineage-specific differentiation. More importantly, alteration of these epigenetic changes would, in many cases, lead to disease generation and even tumour formation. Therefore, it is crucial to elucidate how epigenetic factors, through their interplay with transcriptional regulators, control lineage commitment in hMSCs.
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Affiliation(s)
- Flor M Pérez-Campo
- Department of Internal Medicine, Hospital U. Marqués de Valdecilla-IDIVAL Universidad de Cantabria, 39008 Santander, Cantabria, Spain
| | - José A Riancho
- Department of Internal Medicine, Hospital U. Marqués de Valdecilla-IDIVAL Universidad de Cantabria, 39008 Santander, Cantabria, Spain
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117
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Abstract
A network of reader proteins and enzymes precisely controls gene transcription through the dynamic addition, removal, and recognition of post-translational modifications (PTMs) of histone tails. Histone PTMs work in concert with this network to regulate gene transcription through the histone code, and the dysregulation of PTM maintenance is linked to a large number of diseases, including many types of cancer. A wealth of research aims to elucidate the functions of this code, but our understanding of the effects of PTMs, specifically the methylation of lysine (Lys) and arginine (Arg), is lacking. The development of new tools to study PTMs relies on a sophisticated understanding of the mechanisms that drive protein and small molecule recognition in water. In this review, we outline the physical organic concepts that drive the molecular recognition of Lys and Arg methylation by reader proteins and draw comparisons to the binding mechanisms of small molecule receptors for methylated Lys and Arg that have been developed recently.
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Affiliation(s)
- Joshua E. Beaver
- Department of Chemistry, University of North Carolina, CB 3290, Chapel Hill, North Carolina 27599, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina, CB 3290, Chapel Hill, North Carolina 27599, United States
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118
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Shimojo H, Kawaguchi A, Oda T, Hashiguchi N, Omori S, Moritsugu K, Kidera A, Hiragami-Hamada K, Nakayama JI, Sato M, Nishimura Y. Extended string-like binding of the phosphorylated HP1α N-terminal tail to the lysine 9-methylated histone H3 tail. Sci Rep 2016; 6:22527. [PMID: 26934956 PMCID: PMC4776139 DOI: 10.1038/srep22527] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/15/2016] [Indexed: 11/09/2022] Open
Abstract
The chromodomain of HP1α binds directly to lysine 9-methylated histone H3 (H3K9me). This interaction is enhanced by phosphorylation of serine residues in the N-terminal tail of HP1α by unknown mechanism. Here we show that phosphorylation modulates flexibility of HP1α's N-terminal tail, which strengthens the interaction with H3. NMR analysis of HP1α's chromodomain with N-terminal tail reveals that phosphorylation does not change the overall tertiary structure, but apparently reduces the tail dynamics. Small angle X-ray scattering confirms that phosphorylation contributes to extending HP1α's N-terminal tail. Systematic analysis using deletion mutants and replica exchange molecular dynamics simulations indicate that the phosphorylated serines and following acidic segment behave like an extended string and dynamically bind to H3 basic residues; without phosphorylation, the most N-terminal basic segment of HP1α inhibits interaction of the acidic segment with H3. Thus, the dynamic string-like behavior of HP1α's N-terminal tail underlies the enhancement in H3 binding due to phosphorylation.
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Affiliation(s)
- Hideaki Shimojo
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ayumi Kawaguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Oda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Nobuto Hashiguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Satoshi Omori
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akinori Kidera
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kyoko Hiragami-Hamada
- Division of Genome Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jun-Ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho, Nagoya, Aichi 467-8501, Japan
| | - Mamoru Sato
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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119
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Pinkin NK, N Power A, Waters ML. Late stage modification of receptors identified from dynamic combinatorial libraries. Org Biomol Chem 2015; 13:10939-45. [PMID: 26384269 PMCID: PMC5523513 DOI: 10.1039/c5ob01649e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Small molecule receptors are attractive potential sensors of post-translational modifications, including methylated lysine and methylated arginine. Using dynamic combinatorial chemistry (DCC), our lab previously identified a suite of receptors that bind to Kme3 with a range of affinities ranging from low micromolar to high nanomolar, each with a unique selectivity for Kme3 over the lower methylation states. To enable these receptors to have broad application as Kme3 sensors, we have developed a method for their late-stage modification, which we used to synthesize biotinylated derivatives of A2B, A2D, and A2G in a single step. For our most attractive receptor for applications, A2N, we needed to develop an alternative method for its selective functionalization, which we achieved by "activating" the carboxylic acids on the constituent monomer A or N by pre-functionalizing them with glycine (Gly). Using the resulting Gly-A and Gly-N monomers, we synthesized the novel A2N variants A2Gly-N, Gly-A2N, and Gly-A2Gly-N, which enabled the late stage biotinylation of A2N wherever Gly was incorporated. Finally, we performed ITC and NMR binding experiments to study the effect that carboxylate spacing has on the affinity and selectivity of A2Gly-N and Gly-A2N for KmeX guests compared to A2N. These studies revealed the proximity of the carboxylates to play a complex role in the molecular recognition event, despite their positioning on the outside of the receptor.
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Affiliation(s)
- Nicholas K Pinkin
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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120
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Hu J, Donahue G, Dorsey J, Govin J, Yuan Z, Garcia BA, Shah PP, Berger SL. H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis. Cell Rep 2015; 13:1772-80. [PMID: 26628362 DOI: 10.1016/j.celrep.2015.10.070] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 08/10/2015] [Accepted: 10/24/2015] [Indexed: 01/02/2023] Open
Abstract
Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac) occurring on the nucleosomal lateral surface. We show that H4K44 is acetylated at pre-meiosis and meiosis and displays genome-wide enrichment at recombination hotspots in meiosis. Acetylation at H4K44 is required for normal meiotic recombination, normal levels of double-strand breaks (DSBs) during meiosis, and optimal sporulation. Non-modifiable H4K44R results in increased nucleosomal occupancy around DSB hotspots. Our results indicate that H4K44ac functions to facilitate chromatin accessibility favorable for normal DSB formation and meiotic recombination.
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Affiliation(s)
- Jialei Hu
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Greg Donahue
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean Dorsey
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jérôme Govin
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Laboratoire Biologie à Grande Echelle, INSERM, U1038 Grenoble, France
| | - Zuofei Yuan
- Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Parisha P Shah
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA.
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121
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Kuriya K, Higashiyama E, Avşar-Ban E, Tamaru Y, Ogata S, Takebayashi SI, Ogata M, Okumura K. Direct Visualization of DNA Replication Dynamics in Zebrafish Cells. Zebrafish 2015; 12:432-9. [PMID: 26540100 DOI: 10.1089/zeb.2015.1151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.
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Affiliation(s)
- Kenji Kuriya
- 1 Laboratory of Molecular and Cellular Biology, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Eriko Higashiyama
- 1 Laboratory of Molecular and Cellular Biology, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Eriko Avşar-Ban
- 2 Laboratory for the Utilization of Aquatic Bioresources, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Yutaka Tamaru
- 2 Laboratory for the Utilization of Aquatic Bioresources, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Shin Ogata
- 1 Laboratory of Molecular and Cellular Biology, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
| | - Shin-ichiro Takebayashi
- 3 Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University , Tsu, Japan
| | - Masato Ogata
- 3 Department of Biochemistry and Proteomics, Graduate School of Medicine, Mie University , Tsu, Japan
| | - Katsuzumi Okumura
- 1 Laboratory of Molecular and Cellular Biology, Department of Life Sciences, Graduate School of Bioresources, Mie University , Tsu, Japan
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Sivakumar M, Dineshshankar J, Sunil PM, Nirmal RM, Sathiyajeeva J, Saravanan B, Senthileagappan AR. Stem cells: An insight into the therapeutic aspects from medical and dental perspectives. J Pharm Bioallied Sci 2015; 7:S361-71. [PMID: 26538878 PMCID: PMC4606620 DOI: 10.4103/0975-7406.163453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The recent advancements in the field of stem cell (SC) biology have increased the hope of achieving the definitive treatments for the diseases which are now considered incurable such as diabetes, Parkinson's disease and other chronic long standing conditions. To achieve this possibility, it is necessary to understand the basic concepts of SC biology to utilize in various advanced techniques of regenerative medicine including tissue engineering and gene therapy. This article highlights the types of SCs available and their therapeutic capacity in regenerative medical and dental fields.
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Affiliation(s)
- Muniapillai Sivakumar
- Department of Oral Pathology and Microbiology, Madha Dental College and Hospital, Chennai, Tamil Nadu, India
| | - Janardhanam Dineshshankar
- Department of Oral Pathology and Microbiology, Vivekanandha Dental College for Women, Tiruchengode, Namakkal, Tamil Nadu, India
| | - P M Sunil
- Department of Oral Pathology and Microbiology, Sree Anjaneya Institute of Dental Sciences, Calicut, Kerala, India
| | - R Madhavan Nirmal
- Department of Oral Pathology and Microbiology, Rajah Muthiah Dental College and Hospital, Annamalai University, Chidambaram, Tamil Nadu, India
| | - J Sathiyajeeva
- Department of Oral Pathology and Microbiology, Thai Moogambigai Dental College and Hospital, Chennai, Tamil Nadu, India
| | - Balasubramanian Saravanan
- Department of Oral and Maxillofacial Surgery, Madha Dental College and Hospital, Kundrathur, Chennai, Tamil Nadu, India
| | - A R Senthileagappan
- Department of Pedodontics, Chettinad Dental College and Research Institute, Chettinad Health City, Chennai, Tamil Nadu, India
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123
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Pinkin NK, Liu I, Abron JD, Waters ML. Secondary Binding Interactions in a Synthetic Receptor for Trimethyllysine. Chemistry 2015; 21:17981-6. [DOI: 10.1002/chem.201502302] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Indexed: 01/19/2023]
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124
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An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster. PLoS Genet 2015; 11:e1005523. [PMID: 26389589 PMCID: PMC4577213 DOI: 10.1371/journal.pgen.1005523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 08/22/2015] [Indexed: 11/19/2022] Open
Abstract
RNA surveillance factors are involved in heterochromatin regulation in yeast and plants, but less is known about the possible roles of ribonucleases in the heterochromatin of animal cells. Here we show that RRP6, one of the catalytic subunits of the exosome, is necessary for silencing heterochromatic repeats in the genome of Drosophila melanogaster. We show that a fraction of RRP6 is associated with heterochromatin, and the analysis of the RRP6 interaction network revealed physical links between RRP6 and the heterochromatin factors HP1a, SU(VAR)3-9 and RPD3. Moreover, genome-wide studies of RRP6 occupancy in cells depleted of SU(VAR)3-9 demonstrated that SU(VAR)3-9 contributes to the tethering of RRP6 to a subset of heterochromatic loci. Depletion of the exosome ribonucleases RRP6 and DIS3 stabilizes heterochromatic transcripts derived from transposons and repetitive sequences, and renders the heterochromatin less compact, as shown by micrococcal nuclease and proximity-ligation assays. Such depletion also increases the amount of HP1a bound to heterochromatic transcripts. Taken together, our results suggest that SU(VAR)3-9 targets RRP6 to a subset of heterochromatic loci where RRP6 degrades chromatin-associated non-coding RNAs in a process that is necessary to maintain the packaging of the heterochromatin.
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125
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Juo YY, Gong XJ, Mishra A, Cui X, Baylin SB, Azad NS, Ahuja N. Epigenetic therapy for solid tumors: from bench science to clinical trials. Epigenomics 2015; 7:215-35. [PMID: 25942532 DOI: 10.2217/epi.14.73] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The cancer epigenome is characterized by global DNA methylation and chromatin changes, such as the hypermethylation of specific CpG island promoters. Epigenetic agents like DNA methyltransferase or histone deacetylase inhibitors induce phenotype changes by reactivation of epigenetically silenced tumor suppressor genes. Despite initial promise in hematologic malignancies, epigenetic agents have not shown significant efficacy as monotherapy against solid tumors. Recent trials showed that epigenetic agents exert favorable modifier effects when combined with chemotherapy, hormonal therapy, or other epigenetic agents. Due to the novel nature of their mechanism, it is important to reconsider the optimal patient selection, drug regimen, study design, and outcome measures when pursuing future trials in order to discover the full potential of this new therapeutic modality.
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Affiliation(s)
- Yen-Yi Juo
- Department of Surgery, George Washington University Medical Center, 2150 Pennsylvania Ave. NW, Suite 6B, Washington, DC 20037, USA
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126
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Akiyama T, Xin L, Oda M, Sharov AA, Amano M, Piao Y, Cadet JS, Dudekula DB, Qian Y, Wang W, Ko SBH, Ko MSH. Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells. DNA Res 2015; 22:307-18. [PMID: 26324425 PMCID: PMC4596397 DOI: 10.1093/dnares/dsv013] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/24/2015] [Indexed: 01/06/2023] Open
Abstract
Mouse embryonic stem cells (mESCs) have a remarkable capacity to maintain normal genome stability and karyotype in culture. We previously showed that infrequent bursts of Zscan4 expression (Z4 events) are important for the maintenance of telomere length and genome stability in mESCs. However, the molecular details of Z4 events remain unclear. Here we show that Z4 events involve unexpected transcriptional derepression in heterochromatin regions that usually remain silent. During a Z4 event, we see rapid derepression and rerepression of heterochromatin leading to a burst of transcription that coincides with transient histone hyperacetylation and DNA demethylation, clustering of pericentromeric heterochromatin around the nucleolus, and accumulation of activating and repressive chromatin remodelling complexes. This heterochromatin-based transcriptional activity suggests that mESCs may maintain their extraordinary genome stability at least in part by transiently resetting their heterochromatin.
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Affiliation(s)
- Tomohiko Akiyama
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Li Xin
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Mayumi Oda
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan
| | - Alexei A Sharov
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Misa Amano
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yulan Piao
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - J Scotty Cadet
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yong Qian
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Shigeru B H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan
| | - Minoru S H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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127
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Fina JP, Casati P. HAG3, a Histone Acetyltransferase, Affects UV-B Responses by Negatively Regulating the Expression of DNA Repair Enzymes and Sunscreen Content in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2015; 56:1388-400. [PMID: 25907565 DOI: 10.1093/pcp/pcv054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/02/2015] [Indexed: 05/23/2023]
Abstract
Histone acetylation is regulated by histone acetyltransferases and deacetylases. In Arabidopsis, there are 12 histone acetyltransferases and 18 deacetylases. Histone acetyltransferases are organized in four families: the GNAT/HAG, the MYST, the p300/CBP and the TAFII250 families. Previously, we demonstrated that Arabidopsis mutants in the two members of the MYST acetyltransferase family show increased DNA damage after UV-B irradiation. To investigate further the role of other histone acetyltransferases in UV-B responses, a putative role for enzymes of the GNAT family, HAG1, HAG2 and HAG3, was analyzed. HAG transcripts are not UV-B regulated; however, hag3 RNA interference (RNAi) transgenic plants show a lower inhibition of leaf and root growth by UV-B, higher levels of UV-B-absorbing compounds and less UV-B-induced DNA damage than Wassilewskija (Ws) plants, while hag1 RNAi transgenic plants and hag2 mutants do not show significant differences from wild-type plants. Transcripts for UV-B-regulated genes are highly expressed under control conditions in the absence of UV-B in hag3 RNAi transgenic plants, suggesting that the higher UV-B tolerance may be due to increased levels of proteins that participate in UV-B responses. Together, our data provide evidence that HAG3, directly or indirectly, participates in UV-B-induced DNA damage repair and signaling.
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Affiliation(s)
- Julieta P Fina
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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128
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Abstract
In multicellular organisms differentiated cells must maintain their cellular memory, which will be faithfully inherited and maintained by their progeny. In addition, these specialized cells are exposed to specific environmental and cell-intrinsic signals and will have to appropriately respond to them. Some of these stimuli lead to changes in a subset of genes or to a genome-wide reprogramming of the cells that will remain after stimuli removal and, in some instances, will be inherited by the daughter cells. The molecular substrate that integrates cellular memory and plasticity is the chromatin, a complex of DNA and histones unique to eukaryotes. The nucleosome is the fundamental unit of the chromatin and nucleosomal organization defines different chromatin conformations. Chromatin regulators affect chromatin conformation and accessibility by covalently modifying the DNA or the histones, substituting histone variants, remodeling the nucleosome position or modulating chromatin looping and folding. These regulators frequently act in multiprotein complexes and highly specific interplays among chromatin marks and different chromatin regulators allow a remarkable array of possibilities. Therefore, chromatin regulator nets act to propagate the conformation of different chromatin regions through DNA replication and mitosis, and to remodel the chromatin fiber to regulate the accessibility of the DNA to transcription factors and to the transcription and repair machineries. Here, the state-of-the-art of the best-known chromatin regulators is reviewed.
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129
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Feng L, Chen X. Epigenetic regulation of germ cells-remember or forget? Curr Opin Genet Dev 2015; 31:20-7. [PMID: 25930104 DOI: 10.1016/j.gde.2015.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/02/2015] [Indexed: 12/18/2022]
Abstract
Unlike somatic cells, germ cells retain the potential to reproduce an entire new organism upon fertilization. In order to accomplish the process of fertilization, germ cells undergo an extreme cellular differentiation process known as gametogenesis in order to produce morphologically and functionally distinct oocyte and sperm. In addition to changes in genetic content changes from diploid to haploid, epigenetic mechanisms that modify chromatin state without altering primary DNA sequences have profound influence on germ cell differentiation and moreover, the transgenerational effect. In this review, we will go over the most recent discoveries on epigenetic regulations in germline differentiation and transgenerational inheritance across different metazoan species.
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Affiliation(s)
- Lijuan Feng
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, United States
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, United States.
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130
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Karahan G, Sayar N, Gozum G, Bozkurt B, Konu O, Yulug IG. Relative expression of rRNA transcripts and 45S rDNA promoter methylation status are dysregulated in tumors in comparison with matched-normal tissues in breast cancer. Oncol Rep 2015; 33:3131-45. [PMID: 25962577 DOI: 10.3892/or.2015.3940] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/14/2015] [Indexed: 11/06/2022] Open
Abstract
Ribosomal RNA (rRNA) expression, one of the most important factors regulating ribosome production, is primarily controlled by a CG-rich 45 S rDNA promoter. However, the DNA methylation state of the 45 S rDNA promoter, as well as its effect on rRNA gene expression in types of human cancers is controversial. In the present study we analyzed the methylation status of the rDNA promoter (-380 to +53 bp) as well as associated rRNA expression levels in breast cancer cell lines and breast tumor-normal tissue pairs. We found that the aforementioned regulatory region was extensively methylated (74-96%) in all cell lines and in 68% (13/19 tumor-normal pairs) of the tumors. Expression levels of rRNA transcripts 18 S, 28 S, 5.8 S and 45 S external transcribed spacer (45 S ETS) greatly varied in the breast cancer cell lines regardless of their methylation status. Analyses of rRNA transcript expression levels in the breast tumor and normal matched tissues showed no significant difference when normalized with TBP. On the other hand, using the geometric mean of the rRNA expression values (GM-rRNA) as reference enabled us to identify significant changes in the relative expression of rRNAs in the tissue samples. We propose GM-rRNA normalization as a novel strategy to analyze expression differences between rRNA transcripts. Accordingly, the 18S rRNA/GM-rRNA ratio was significantly higher whereas the 5.8S rRNA/GM-rRNA ratio was significantly lower in breast tumor samples than this ratio in the matched normal samples. Moreover, the 18S rRNA/GM-rRNA ratio was negatively correlated with the 45 S rDNA promoter methylation level in the normal breast tissue samples, yet not in the breast tumors. Significant correlations observed between the expression levels of rRNA transcripts in the normal samples were lost in the tumor samples. We showed that the expression of rRNA transcripts may not be based solely on promoter methylation. Carcinogenesis may cause dysregulation of the correlation between spliced rRNA expression levels, possibly due to changes in rRNA processing, which requires further investigation.
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Affiliation(s)
- Gurbet Karahan
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Nilufer Sayar
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Gokcen Gozum
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Betul Bozkurt
- Department of General Surgery, Ankara Numune Research and Teaching Hospital, TR-06100 Ankara, Turkey
| | - Ozlen Konu
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
| | - Isik G Yulug
- Department of Molecular Biology and Genetics, Bilkent University, Faculty of Science, TR-06800 Ankara, Turkey
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131
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Barbieri M. Semantic Biology and the Mind-Body Problem: The Theory of the Conventional Mind. ACTA ACUST UNITED AC 2015. [DOI: 10.1162/biot.2006.1.4.352] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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132
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Affiliation(s)
- Manuel M. Müller
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
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133
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Meta A, Hirashima M, Imamura T, Kawamura R, Yano K, Uehara K, Nakashima T. High-yield preparation of recombinant human α-thrombin for therapeutic use. J Biosci Bioeng 2015; 120:432-7. [PMID: 25735923 DOI: 10.1016/j.jbiosc.2015.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 10/23/2022]
Abstract
In this study, we established stable cell lines producing 1.5 mg/mL recombinant human prothrombin in 400-L fed-batch culture, using CHO DG44 cells as a host cell line. And we also established a recombinant human α-thrombin purification process that produces a purified product suitable for use as a biopharmaceutical, by using recombinant ecarin from CHO DG44 cells, achieving a total yield of approximately 27% of prothrombin in culture medium. The establishment of stable cell lines with high expression levels, long-term passage stability and satisfactory scale-up are essential to ensure the stable supply of biopharmaceuticals. Furthermore, biopharmaceuticals must be of high quality to assure safety and effectiveness in target applications. We had previously reported that recombinant human prethrombin-2 expression level in a stable cell line established using the mouse myeloma cells, Sp2/0-Ag14, reached 200 μg/mL using animal-free materials in 50-L fed-batch culture. However, the productivity was insufficient to completely replace α-thrombin in human plasma preparations. By employing CHO DG44 cells as a host cell line, we had established a stable cell line and achieved significant improvements in quality, productivity of recombinant human α-thrombin manufacture suitable for use as a biopharmaceutical.
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Affiliation(s)
- Akihiro Meta
- R&D Division, The Chemo-Sero-Therapeutic Research Institute, KAKETSUKEN, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan
| | - Masaki Hirashima
- R&D Division, The Chemo-Sero-Therapeutic Research Institute, KAKETSUKEN, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan
| | - Takayuki Imamura
- R&D Division, The Chemo-Sero-Therapeutic Research Institute, KAKETSUKEN, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan
| | - Ryoichi Kawamura
- R&D Division, The Chemo-Sero-Therapeutic Research Institute, KAKETSUKEN, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan
| | - Kentaro Yano
- Blood Plasma Division, The Chemo-Sero-Therapeutic Research Institute, KAKETSUKEN, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan
| | - Kenji Uehara
- R&D Division, The Chemo-Sero-Therapeutic Research Institute, KAKETSUKEN, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan
| | - Toshihiro Nakashima
- R&D Division, The Chemo-Sero-Therapeutic Research Institute, KAKETSUKEN, 1314-1 Kyokushi-Kawabe, Kikuchi, Kumamoto 869-1298, Japan.
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134
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Audano M, Ferrari A, Fiorino E, Kuenzl M, Caruso D, Mitro N, Crestani M, De Fabiani E. Energizing Genetics and Epi-genetics: Role in the Regulation of Mitochondrial Function. Curr Genomics 2015; 15:436-56. [PMID: 25646072 PMCID: PMC4311388 DOI: 10.2174/138920291506150106151119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/11/2014] [Accepted: 11/18/2014] [Indexed: 12/15/2022] Open
Abstract
Energy metabolism and mitochondrial function hold a core position in cellular homeostasis. Oxidative metabolism is regulated at multiple levels, ranging from gene transcription to allosteric modulation. To accomplish the fine tuning of these multiple regulatory circuits, the nuclear and mitochondrial compartments are tightly and reciprocally controlled. The fact that nuclear encoded factors, PPARγ coactivator 1α and mitochondrial transcription factor A, play pivotal roles in the regulation of oxidative metabolism and mitochondrial biogenesis is paradigmatic of this crosstalk. Here we provide an updated survey of the genetic and epigenetic mechanisms involved in the control of energy metabolism and mitochondrial function. Chromatin dynamics highly depends on post-translational modifications occurring at specific amino acids in histone proteins and other factors associated to nuclear DNA. In addition to the well characterized enzymes responsible for histone methylation/demethylation and acetylation/deacetylation, other factors have gone on the "metabolic stage". This is the case of the new class of α-ketoglutarate-regulated demethylases (Jumonji C domain containing demethylases) and of the NAD+-dependent deacetylases, also known as sirtuins. Moreover, unexpected features of the machineries involved in mitochondrial DNA (mtDNA) replication and transcription, mitochondrial RNA processing and maturation have recently emerged. Mutations or defects of any component of these machineries profoundly affect mitochondrial activity and oxidative metabolism. Finally, recent evidences support the importance of mtDNA packaging in replication and transcription. These observations, along with the discovery that non-classical CpG islands present in mtDNA undergo methylation, indicate that epigenetics also plays a role in the regulation of the mitochondrial genome function.
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Affiliation(s)
- Matteo Audano
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Alessandra Ferrari
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Erika Fiorino
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Martin Kuenzl
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Donatella Caruso
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Nico Mitro
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Maurizio Crestani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Italy
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135
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Sekar TV, Foygel K, Devulapally R, Paulmurugan R. Degron protease blockade sensor to image epigenetic histone protein methylation in cells and living animals. ACS Chem Biol 2015; 10:165-74. [PMID: 25489787 PMCID: PMC4301175 DOI: 10.1021/cb5008037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Lysine
methylation of histone H3 and H4 has been identified as
a promising therapeutic target in treating various cellular diseases.
The availability of an in vivo assay that enables
rapid screening and preclinical evaluation of drugs that potentially
target this cellular process will significantly expedite the pace
of drug development. This study is the first to report the development
of a real-time molecular imaging biosensor (a fusion protein, [FLuc2]-[Suv39h1]-[(G4S)3]-[H3-K9]-[cODC]) that can detect and monitor the methylation
status of a specific histone lysine methylation mark (H3-K9) in live
animals. The sensitivity of this sensor was assessed in various cell
lines, in response to down-regulation of methyltransferase EHMT2 by
specific siRNA, and in nude mice with lysine replacement mutants. In vivo imaging in response to a combination of methyltransferase
inhibitors BIX01294 and Chaetocin in mice reveals the potential of
this sensor for preclinical drug evaluation. This biosensor thus has
demonstrated its utility in the detection of H3-K9 methylations in vivo and potential value in preclinical drug development.
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Affiliation(s)
- Thillai V. Sekar
- Molecular Imaging Program
at Stanford, Bio-X Program, Stanford University School of Medicine, Stanford, California, United States
| | - Kira Foygel
- Molecular Imaging Program
at Stanford, Bio-X Program, Stanford University School of Medicine, Stanford, California, United States
| | - Rammohan Devulapally
- Molecular Imaging Program
at Stanford, Bio-X Program, Stanford University School of Medicine, Stanford, California, United States
| | - Ramasamy Paulmurugan
- Molecular Imaging Program
at Stanford, Bio-X Program, Stanford University School of Medicine, Stanford, California, United States
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136
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Zhu M, Li Y, Chen G, Ren L, Xie Q, Zhao Z, Hu Z. Silencing SlELP2L, a tomato Elongator complex protein 2-like gene, inhibits leaf growth, accelerates leaf, sepal senescence, and produces dark-green fruit. Sci Rep 2015; 5:7693. [PMID: 25573793 PMCID: PMC4287726 DOI: 10.1038/srep07693] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/28/2014] [Indexed: 11/12/2022] Open
Abstract
The multi-subunit complex Elongator interacts with elongating RNA polymerase II (RNAPII) and is thought to facilitate transcription through histone acetylation. Elongator is highly conserved in eukaryotes, yet has multiple kingdom-specific functions in diverse organisms. Recent genetic studies performed in Arabidopsis have demonstrated that Elongator functions in plant growth and development, and in response to biotic and abiotic stress. However, little is known about its roles in other plant species. Here, we study the function of an Elongator complex protein 2-like gene in tomato, here designated as SlELP2L, through RNAi-mediated gene silencing. Silencing SlELP2L in tomato inhibits leaf growth, accelerates leaf and sepal senescence, and produces dark-green fruit with reduced GA and IAA contents in leaves, and increased chlorophyll accumulation in pericarps. Gene expression analysis indicated that SlELP2L-silenced plants had reduced transcript levels of ethylene- and ripening-related genes during fruit ripening with slightly decreased carotenoid content in fruits, while the expression of DNA methyltransferase genes was up-regulated, indicating that SlELP2L may modulate DNA methylation in tomato. Besides, silencing SlELP2L increases ABA sensitivity in inhibiting seedling growth. These results suggest that SlELP2L plays important roles in regulating plant growth and development, as well as in response to ABA in tomato.
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Affiliation(s)
- Mingku Zhu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Yali Li
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Guoping Chen
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Lijun Ren
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Qiaoli Xie
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Zhiping Zhao
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
| | - Zongli Hu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, People's Republic of China
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137
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Abstract
Diverse classes of RNA, ranging from small to long non-coding RNAs, have emerged as key regulators of gene expression, genome stability and defence against foreign genetic elements. Small RNAs modify chromatin structure and silence transcription by guiding Argonaute-containing complexes to complementary nascent RNA scaffolds and then mediating the recruitment of histone and DNA methyltransferases. In addition, recent advances suggest that chromatin-associated long non-coding RNA scaffolds also recruit chromatin-modifying complexes independently of small RNAs. These co-transcriptional silencing mechanisms form powerful RNA surveillance systems that detect and silence inappropriate transcription events, and provide a memory of these events via self-reinforcing epigenetic loops.
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Affiliation(s)
- Daniel Holoch
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Danesh Moazed
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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138
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Banaei-Moghaddam AM, Martis MM, Macas J, Gundlach H, Himmelbach A, Altschmied L, Mayer KF, Houben A. Genes on B chromosomes: Old questions revisited with new tools. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:64-70. [DOI: 10.1016/j.bbagrm.2014.11.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 12/21/2022]
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139
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Translational implications of the β-cell epigenome in diabetes mellitus. Transl Res 2015; 165:91-101. [PMID: 24686035 PMCID: PMC4162854 DOI: 10.1016/j.trsl.2014.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/04/2014] [Accepted: 03/06/2014] [Indexed: 12/12/2022]
Abstract
Diabetes mellitus is a disorder of glucose homeostasis that affects more than 24 million Americans and 382 million individuals worldwide. Dysregulated insulin secretion from the pancreatic β cells plays a central role in the pathophysiology of all forms of diabetes mellitus. Therefore, an enhanced understanding of the pathways that contribute to β-cell failure is imperative. Epigenetics refers to heritable changes in DNA transcription that occur in the absence of changes to the linear DNA nucleotide sequence. Recent evidence suggests an expanding role of the β-cell epigenome in the regulation of metabolic health. The goal of this review is to discuss maladaptive changes in β-cell DNA methylation patterns and chromatin architecture, and their contribution to diabetes pathophysiology. Efforts to modulate the β-cell epigenome as a means to prevent, diagnose, and treat diabetes are also discussed.
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140
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Cao HX, Vu GTH, Wang W, Messing J, Schubert I. Chromatin organisation in duckweed interphase nuclei in relation to the nuclear DNA content. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17 Suppl 1:120-4. [PMID: 24853858 DOI: 10.1111/plb.12194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 03/13/2014] [Indexed: 05/23/2023]
Abstract
The accessibility of DNA during fundamental processes, such as transcription, replication and DNA repair, is tightly modulated through a dynamic chromatin structure. Differences in large-scale chromatin structure at the microscopic level can be observed as euchromatic and heterochromatic domains in interphase nuclei. Here, key epigenetic marks, including histone H3 methylation and 5-methylcytosine (5-mC) as a DNA modification, were studied cytologically to describe the chromatin organisation of representative species of the five duckweed genera in the context of their nuclear DNA content, which ranged from 158 to 1881 Mbp. All studied duckweeds, including Spirodela polyrhiza with a genome size and repeat proportion similar to that of Arabidopsis thaliana, showed dispersed distribution of heterochromatin signatures (5mC, H3K9me2 and H3K27me1). This immunolabelling pattern resembles that of early developmental stages of Arabidopsis nuclei, with less pronounced heterochromatin chromocenters and heterochromatic marks weakly dispersed throughout the nucleus.
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Affiliation(s)
- H X Cao
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Germany
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141
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Sekar TV, Foygel K, Gelovani JG, Paulmurugan R. Genetically encoded molecular biosensors to image histone methylation in living animals. Anal Chem 2014; 87:892-9. [PMID: 25506787 PMCID: PMC4303335 DOI: 10.1021/ac502629r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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Post-translational addition of methyl
groups to the amino terminal
tails of histone proteins regulates cellular gene expression at various
stages of development and the pathogenesis of cellular diseases, including
cancer. Several enzymes that modulate these post-translational modifications
of histones are promising targets for development of small molecule
drugs. However, there is no promising real-time histone methylation
detection tool currently available to screen and validate potential
small molecule histone methylation modulators in small animal models.
With this in mind, we developed genetically encoded molecular biosensors
based on the split-enzyme complementation approach for in vitro and
in vivo imaging of lysine 9 (H3–K9 sensor) and lysine 27 (H3–K27
sensor) methylation marks of histone 3. These methylation sensors
were validated in vitro in HEK293T, HepG2, and HeLa cells. The efficiency
of the histone methylation sensor was assessed by employing methyltransferase
inhibitors (Bix01294 and UNC0638), demethylase inhibitor (JIB-04),
and siRNA silencing at the endogenous histone K9-methyltransferase
enzyme level. Furthermore, noninvasive bioluminescence imaging of
histone methylation sensors confirmed the potential of these sensors
in monitoring histone methylation status in response to histone methyltransferase
inhibitors in living animals. Experimental results confirmed that
the developed H3–K9 and H3–K27 sensors are specific
and sensitive to image the drug-induced histone methylation changes
in living animals. These novel histone methylation sensors can facilitate
the in vitro screening and in vivo characterization of new histone
methyltransferase inhibitors and accelerate the pace of introduction
of epigenetic therapies into the clinic.
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Affiliation(s)
- Thillai V Sekar
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine , 318 Campus Drive, East Wing, 1st Floor, Stanford, California 94305, United States
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142
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Romero-Fernández I, Casas-Delucchi CS, Cano-Linares M, Arroyo M, Sánchez A, Cardoso MC, Marchal JA. Epigenetic modifications in sex heterochromatin of vole rodents. Chromosoma 2014; 124:341-51. [PMID: 25527445 DOI: 10.1007/s00412-014-0502-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/05/2014] [Accepted: 12/05/2014] [Indexed: 11/26/2022]
Abstract
The genome of some vole rodents contains large blocks of heterochromatin coupled to the sex chromosomes. While the DNA content of these heterochromatic blocks has been extensively analyzed, little is known about the epigenetic modifications controlling their structure and dynamics. To better understand its organization and functions within the nucleus, we have compared the distribution pattern of several epigenetic marks in cells from two species, Microtus agrestis and Microtus cabrerae. We first could show that the heterochromatic blocks are identifiable within the nuclei due to their AT enrichment detectable by DAPI staining. By immunostaining analyses, we demonstrated that enrichment in H3K9me3 and HP1, depletion of DNA methylation as well as H4K8ac and H3K4me2, are major conserved epigenetic features of this heterochromatin in both sex chromosomes. Furthermore, we provide evidence of transcriptional activity for some repeated DNAs in cultivated cells. These transcripts are partially polyadenylated and their levels are not altered during mitotic arrest. In summary, we show here that enrichment in H3K9me3 and HP1, DNA demethylation, and transcriptional activity are major epigenetic features of sex heterochromatin in vole rodents.
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Affiliation(s)
- I Romero-Fernández
- Department of Experimental Biology, University of Jaén, Jaén, E-23071, Spain
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143
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Garrigues JM, Sidoli S, Garcia BA, Strome S. Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2. Genome Res 2014; 25:76-88. [PMID: 25467431 PMCID: PMC4317175 DOI: 10.1101/gr.180489.114] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Formation of heterochromatin serves a critical role in organizing the genome and regulating gene expression. In most organisms, heterochromatin flanks centromeres and telomeres. To identify heterochromatic regions in the heavily studied model C. elegans, which possesses holocentric chromosomes with dispersed centromeres, we analyzed the genome-wide distribution of the heterochromatin protein 1 (HP1) ortholog HPL-2 and compared its distribution to other features commonly associated with heterochromatin. HPL-2 binding highly correlates with histone H3 mono- and dimethylated at lysine 9 (H3K9me1 and H3K9me2) and forms broad domains on autosomal arms. Although HPL-2, like other HP1 orthologs, binds H3K9me peptides in vitro, the distribution of HPL-2 in vivo appears relatively normal in mutant embryos that lack H3K9me, demonstrating that the chromosomal distribution of HPL-2 can be achieved in an H3K9me-independent manner. Consistent with HPL-2 serving roles independent of H3K9me, hpl-2 mutant worms display more severe defects than mutant worms lacking H3K9me. HPL-2 binding is enriched for repetitive sequences, and on chromosome arms is anticorrelated with centromeres. At the genic level, HPL-2 preferentially associates with well-expressed genes, and loss of HPL-2 results in up-regulation of some binding targets and down-regulation of others. Our work defines heterochromatin in an important model organism and uncovers both shared and distinctive properties of heterochromatin relative to other systems.
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Affiliation(s)
- Jacob M Garrigues
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Simone Sidoli
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Susan Strome
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA;
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144
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Tethering of SUUR and HP1 proteins results in delayed replication of euchromatic regions in Drosophila melanogaster polytene chromosomes. Chromosoma 2014; 124:209-20. [PMID: 25398563 DOI: 10.1007/s00412-014-0491-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/14/2014] [Accepted: 10/28/2014] [Indexed: 12/19/2022]
Abstract
We analyze how artificial targeting of Suppressor of Under-Replication (SUUR) and HP1 proteins affects DNA replication in the "open," euchromatic regions. Normally these regions replicate early in the S phase and display no binding of either SUUR or HP1. These proteins were expressed as fusions with DNA-binding domain of GAL4 and recruited to multimerized UAS integrated in three euchromatic sites of the polytene X chromosome: 3B, 8D, and 18B. Using PCNA staining as a marker of ongoing replication, we showed that targeting of SUUR(GAL4DBD) and HP1(GAL4DBD) results in delayed replication of appropriate euchromatic regions. Specifically, replication at these regions starts early, much like in the absence of the fusion proteins; however, replication completion is significantly delayed. Notably, delayed replication was insufficient to induce underreplication. Recruitment of SUUR(GAL4DBD) and HP1(GAL4DBD) had distinct effects on expression of a mini-white reporter, found near UAS. Whereas SUUR(GAL4DBD) had no measurable influence on mini-white expression, HP1(GAL4DBD) targeting silenced mini-white, even in the absence of functional SU(VAR)3-9. Furthermore, recruitment of SUUR(GAL4DBD) and HP1(GAL4DBD) had distinct effects on the protein composition of target regions. HP1(GAL4DBD) but not SUUR(GAL4DBD) could displace an open chromatin marker, CHRIZ, from the tethering sites.
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145
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Nishibuchi G, Machida S, Osakabe A, Murakoshi H, Hiragami-Hamada K, Nakagawa R, Fischle W, Nishimura Y, Kurumizaka H, Tagami H, Nakayama JI. N-terminal phosphorylation of HP1α increases its nucleosome-binding specificity. Nucleic Acids Res 2014; 42:12498-511. [PMID: 25332400 PMCID: PMC4227797 DOI: 10.1093/nar/gku995] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/09/2014] [Accepted: 10/06/2014] [Indexed: 01/08/2023] Open
Abstract
Heterochromatin protein 1 (HP1) is an evolutionarily conserved chromosomal protein that binds to lysine 9-methylated histone H3 (H3K9me), a hallmark of heterochromatin. Although HP1 phosphorylation has been described in several organisms, the biological implications of this modification remain largely elusive. Here we show that HP1's phosphorylation has a critical effect on its nucleosome binding properties. By in vitro phosphorylation assays and conventional chromatography, we demonstrated that casein kinase II (CK2) is the kinase primarily responsible for phosphorylating the N-terminus of human HP1α. Pull-down assays using in vitro-reconstituted nucleosomes showed that unmodified HP1α bound H3K9-methylated and H3K9-unmethylated nucleosomes with comparable affinity, whereas CK2-phosphorylated HP1α showed a high specificity for H3K9me3-modified nucleosomes. Electrophoretic mobility shift assays showed that CK2-mediated phosphorylation diminished HP1α's intrinsic DNA binding, which contributed to its H3K9me-independent nucleosome binding. CK2-mediated phosphorylation had a similar effect on the nucleosome-binding specificity of fly HP1a and S. pombe Swi6. These results suggested that HP1 phosphorylation has an evolutionarily conserved role in HP1's recognition of H3K9me-marked nucleosomes.
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Affiliation(s)
- Gohei Nishibuchi
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiromu Murakoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kyoko Hiragami-Hamada
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Reiko Nakagawa
- Proteomics Support Unit, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hideaki Tagami
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
| | - Jun-ichi Nakayama
- Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
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146
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Stępiński D. Functional ultrastructure of the plant nucleolus. PROTOPLASMA 2014; 251:1285-306. [PMID: 24756369 PMCID: PMC4209244 DOI: 10.1007/s00709-014-0648-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/08/2014] [Indexed: 05/23/2023]
Abstract
Nucleoli are nuclear domains present in almost all eukaryotic cells. They not only specialize in the production of ribosomal subunits but also play roles in many fundamental cellular activities. Concerning ribosome biosynthesis, particular stages of this process, i.e., ribosomal DNA transcription, primary RNA transcript processing, and ribosome assembly proceed in precisely defined nucleolar subdomains. Although eukaryotic nucleoli are conservative in respect of their main function, clear morphological differences between these structures can be noticed between individual kingdoms. In most cases, a plant nucleolus shows well-ordered structure in which four main ultrastructural components can be distinguished: fibrillar centers, dense fibrillar component, granular component, and nucleolar vacuoles. Nucleolar chromatin is an additional crucial structural component of this organelle. Nucleolonema, although it is not always an unequivocally distinguished nucleolar domain, has often been described as a well-grounded morphological element, especially of plant nucleoli. The ratios and morphology of particular subcompartments of a nucleolus can change depending on its metabolic activity which in turn is correlated with the physiological state of a cell, cell type, cell cycle phase, as well as with environmental influence. Precise attribution of functions to particular nucleolar subregions in the process of ribosome biosynthesis is now possible using various approaches. The presented description of plant nucleolar morphology summarizes previous knowledge regarding the function of nucleoli as well as of their particular subdomains not only in the course of ribosome biosynthesis.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland,
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147
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The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proc Natl Acad Sci U S A 2014; 111:16166-71. [PMID: 25344531 DOI: 10.1073/pnas.1418564111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48A(NPL4) complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.
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148
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Rodrigues HF, Souza TA, Ghiraldini FG, Mello MLS, Moraes AS. Increased age is associated with epigenetic and structural changes in chromatin from neuronal nuclei. J Cell Biochem 2014; 115:659-65. [PMID: 24166948 DOI: 10.1002/jcb.24705] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/22/2013] [Indexed: 01/06/2023]
Abstract
Chromatin organization has been considered to play a major role on aging, by regulating DNA accessibility to transcription and repair machinery. Such organization can be modulated by epigenetic events, such as DNA methylation and histone post-translational modifications. Since changes on gene expression profiles have been described in aged neurons, our aim was to study the age-dependent relationship between structural and epigenetic alterations on chromatin of cortical neurons from mice. For this purpose, isolated neuronal nuclei from mice of two ages were studied by image analysis after cytochemistry, or assessed for chromatin accessibility by enzymatic digestion. Additionally, two epigenetic marks, for open and for densely packed chromatin fibers were quantified. Results indicate epigenetically driven alterations on chromatin organization of cortical neurons with advancing age, whose fibers seem to undergo redistribution and unpackaging. Since increased transcriptional activity is not characteristic of aged neurons, these loosened chromatin fibers may be associated with impaired genome stability, as well as with increased accessibility of repair machinery to a life span damaged DNA.
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Affiliation(s)
- Henrique F Rodrigues
- Cytology, Histology, and Embryology Section, Institute of Biomedical Sciences, Federal University of Uberlandia (UFU), Uberlandia, Minas Gerais, 38400-902, Brazil
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149
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Page A, Mann DA, Mann J. The mechanisms of HSC activation and epigenetic regulation of HSCs phenotypes. CURRENT PATHOBIOLOGY REPORTS 2014; 2:163-170. [PMID: 27413631 DOI: 10.1007/s40139-014-0052-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Epigenetics is a dynamically expanding field of science entailing numerous regulatory mechanisms controlling changes of gene expression in response to environmental factors. Over the recent years there has been a great interest in epigenetic marks as a potential diagnostic and prognostic tool or future target for treatment of various human diseases. There is an increasing body of published research to suggest that epigenetic events regulate progression of chronic liver disease. Experimental manipulation of epigenetic signatures such as DNA methylation, histone acetylation / methylation and the activities of proteins that either annotate or interpret these epigenetic marks can have profound effects on the activation and phenotype of HSC, key cells responsible for onset and progression of liver fibrosis. This review presents recent advances in epigenetic alterations, which could provide mechanistic insight into the pathogenesis of chronic liver disease and provide novel clinical applications.
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Affiliation(s)
- Agata Page
- Institute of Cellular Medicine, Faculty of Medical Sciences, 4 Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Derek A Mann
- Institute of Cellular Medicine, Faculty of Medical Sciences, 4 Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Jelena Mann
- Institute of Cellular Medicine, Faculty of Medical Sciences, 4 Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
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150
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Upadhyay M, Priya GK, Ramesh P, Madhavi MB, Rath S, Bal V, George A, Vaidya T. CD40 signaling drives B lymphocytes into an intermediate memory-like state, poised between naïve and plasma cells. J Cell Physiol 2014; 229:1387-96. [PMID: 24482285 DOI: 10.1002/jcp.24572] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/16/2014] [Indexed: 01/18/2023]
Abstract
Immunological memory comprising of antigen-specific B and T cells contributes to the acquisition of long-term resistance to pathogens. Interactions between CD40 on B cells and CD40L on T cells are responsible for several aspects of acquired immune responses including generation of memory B cells. In order to gain insights into events leading to memory B cell formation, we analyzed the genome-wide expression profile of murine naive B cells stimulated in the presence of anti-CD40. We have identified over 8,000 genes whose expression is altered minimally 1.5-fold at least at one time point over a 3-day time course. The array analysis indicates that changes in expression level of maximum number of these genes occur within 24 h of anti-CD40 treatment. In parallel, we have studied the events following CD40 ligation by examining the expression of known regulators of naive B cell to plasma cell transition, including Pax5 and BLIMP1. The expression profile of these regulatory genes indicates firstly, that CD40 signaling activates naïve B cells to a phenotype that is intermediate between the naive and plasma cell stages of the B cell differentiation. Secondly, the major known regulator of plasma cell differentiation, BLIMP1, gets irreversibly downregulated upon anti-CD40 treatment. Additionally, our data reveal that CD40 signaling mediated BLIMP1 downregulation occurs by non-Pax5/non-Bcl6 dependent mechanisms, indicating novel mechanisms at work that add to the complexity of understanding of B cell master regulatory molecules like BLIMP1 and Pax5.
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Affiliation(s)
- Mala Upadhyay
- Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
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