101
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Hu Y, Lai Y, Chen X, Zhou DX, Zhao Y. Distribution pattern of histone marks potentially determines their roles in transcription and RNA processing in rice. JOURNAL OF PLANT PHYSIOLOGY 2020; 249:153167. [PMID: 32353606 DOI: 10.1016/j.jplph.2020.153167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 04/12/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
Histone marks including histone modifications and histone variants may affect the processes of gene transcription and co-transcriptional RNA processing depending on their specific deposition patterns within genes. Here, we analyzed distribution patterns of rice histone marks and divided them into seven clusters according to their enrichment in promoter, transcription start site (TSS), and gene body regions. Expression levels of the genes in each cluster were explored to disclose the importance of histone marks in the processes of transcription. We show that: a) H3K4me3 and histone acetylation marks show locally different distributions at TSS, implying that they may play different roles in transcription initiation. b) H3K36me1 enriched at TSS has a negative effect on transcription. c) Genes with high level of expression were marked by H3K36me3 at both the TSS and body regions. In addition, we found that H3K4me2, H3K23ac, H3K4ac, and H2A.Z show exon-biased enrichment, suggesting they may be chromatin marks involved in co-transcriptional splicing. Finally, we identified histone marks that discriminate constitutive expression genes (CEGs) from tissue-specific expressed genes (TSEGs). Taken together, the analysis revealed distribution patterns of different histone marks in rice to infer their potential roles in transcription and RNA processing. The results lay foundation for further understanding the mechanism by which histone marks are involved in the regulation of these processes in plants.
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Affiliation(s)
- Yongfeng Hu
- College of Bioengineering, Jingchu University of Technology, 448000, Jingmen, China.
| | - Yan Lai
- College of Bioengineering, Jingchu University of Technology, 448000, Jingmen, China
| | - Xiangsong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, 430072, Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China; University Paris-Saclay, CNRS, INRAE, Institute of Plant Science of Paris-Saclay (IPS2), 91405, Orsay, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China.
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102
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Zhang L, Xu W, Gao X, Li W, Qi S, Guo D, Ajayi OE, Ding SW, Wu Q. lncRNA Sensing of a Viral Suppressor of RNAi Activates Non-canonical Innate Immune Signaling in Drosophila. Cell Host Microbe 2020; 27:115-128.e8. [PMID: 31917956 DOI: 10.1016/j.chom.2019.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/10/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022]
Abstract
Antiviral immunity in insects is mediated by the RNA interference (RNAi) pathway. Viruses evade antiviral RNAi by expressing virulence factors known as viral suppressors of RNAi (VSR). Here, we report the identification of VINR, a Drosophila VSR-interacting long non-coding (lnc) RNA that activates non-canonical innate immune signaling upon detection of the dsRNA-binding VSR of Drosophila C virus (DCV). VINR is required for the induction of antimicrobial peptide (AMP) genes but dispensable for antiviral RNAi. VINR functions by preventing the ubiquitin proteasome-dependent degradation of Cactin, a coiled-coil and arginine-serine-rich domain-containing protein that regulates a non-cannonical antimicrobial pathway for AMP induction. CRISPR-Cas9 knockout of VINR in Drosophila cells enhances DCV replication independently of antiviral RNAi, and VINR-knockout adult flies exhibit enhanced disease susceptibility to DCV and bacteria. Our findings reveal a counter counter-defense strategy activated by a lncRNA in response to the viral suppression of the primary antiviral RNAi immunity.
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Affiliation(s)
- Liqin Zhang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wen Xu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xinlei Gao
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wenjie Li
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Shuishui Qi
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Dongyang Guo
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Olugbenga Emmanuel Ajayi
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Shou-Wei Ding
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside CA, USA
| | - Qingfa Wu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
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103
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Yi D, Nguyen HP, Sul HS. Epigenetic dynamics of the thermogenic gene program of adipocytes. Biochem J 2020; 477:1137-1148. [PMID: 32219439 PMCID: PMC8594062 DOI: 10.1042/bcj20190599] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
Brown adipose tissue (BAT) is a metabolically beneficial organ capable of burning fat by dissipating chemical energy into heat, thereby increasing energy expenditure. Moreover, subcutaneous white adipose tissue can undergo so-called browning/beiging. The recent recognition of the presence of brown or beige adipocytes in human adults has attracted much attention to elucidate the molecular mechanism underlying the thermogenic adipose program. Many key transcriptional regulators critical for the thermogenic gene program centering on activating the UCP1 promoter, have been discovered. Thermogenic gene expression in brown adipocytes rely on co-ordinated actions of a multitude of transcription factors, including EBF2, PPARγ, Zfp516 and Zc3h10. These transcription factors probably integrate into a cohesive network for BAT gene program. Moreover, these transcription factors recruit epigenetic factors, such as LSD1 and MLL3/4, for specific histone signatures to establish the favorable chromatin landscape. In this review, we discuss advances made in understanding the molecular mechanism underlying the thermogenic gene program, particularly epigenetic regulation.
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Affiliation(s)
- Danielle Yi
- Department of Nutritional Sciences and Toxicology and Endocrinology Program, University of California, Berkeley, CA 94720, U.S.A
| | - Hai P Nguyen
- Department of Nutritional Sciences and Toxicology and Endocrinology Program, University of California, Berkeley, CA 94720, U.S.A
| | - Hei Sook Sul
- Department of Nutritional Sciences and Toxicology and Endocrinology Program, University of California, Berkeley, CA 94720, U.S.A
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104
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Crespo-Salvador Ó, Sánchez-Giménez L, López-Galiano MJ, Fernández-Crespo E, Schalschi L, García-Robles I, Rausell C, Real MD, González-Bosch C. The Histone Marks Signature in Exonic and Intronic Regions Is Relevant in Early Response of Tomato Genes to Botrytis cinerea and in miRNA Regulation. PLANTS 2020; 9:plants9030300. [PMID: 32121544 PMCID: PMC7154849 DOI: 10.3390/plants9030300] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/31/2022]
Abstract
Research into the relationship between epigenetic regulation and resistance to biotic stresses provides alternatives for plant protection and crop improvement. To unravel the mechanisms underlying tomato responses to Botrytis cinerea, we performed a chromatin immunoprecipitation (ChIP) analysis showing the increase in H3K9ac mark along the early induced genes SlyDES, SlyDOX1, and SlyLoxD encoding oxylipin-pathway enzymes, and SlyWRKY75 coding for a transcriptional regulator of hormonal signaling. This histone mark showed a more distinct distribution than the previously studied H3K4me3. The RNAPol-ChIP analysis reflected the actual gene transcription associated with increased histone modifications. A different pattern of marks in the oxylipin-related genes against P. syringae supported a pathogen-specific profile, while no significant differences occurred in SlyWRKY75. The epigenetic regulation of SlyWRKY75 by the intron-binding miR1127-3p was supported by the presence of SlyWRKY75 pre-mRNA in control plants. Interestingly, mRNA was found to be accumulated in response to B. cinerea and P. syringae, while reduction in miRNA only occurred against B. cinerea. The intronic region presented a similar pattern of marks than the rest of the gene in both pathosystems, except for H3K4me3 in the miRNA binding site upon B. cinerea. We located the gene encoding Sly-miR1127-3p, which presented reduced H3K4me3 on its promoter against B. cinerea.
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Affiliation(s)
- Óscar Crespo-Salvador
- Department of Biochemistry and Molecular Biology, University of Valencia, Agrochemical and Food Technology Institute (CSIC), 46980 Paterna, Valencia, Spain; (Ó.C.-S.); (L.S.-G.)
| | - Lorena Sánchez-Giménez
- Department of Biochemistry and Molecular Biology, University of Valencia, Agrochemical and Food Technology Institute (CSIC), 46980 Paterna, Valencia, Spain; (Ó.C.-S.); (L.S.-G.)
| | - Mª José López-Galiano
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - Emma Fernández-Crespo
- Plant Physiology Area, Biochemistry and Biotechnology Group, Department CAMN, University Jaume I, 12071 Castellón, Spain; (E.F.-C.); (L.S.)
| | - Loredana Schalschi
- Plant Physiology Area, Biochemistry and Biotechnology Group, Department CAMN, University Jaume I, 12071 Castellón, Spain; (E.F.-C.); (L.S.)
| | - Inmaculada García-Robles
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - Carolina Rausell
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - M Dolores Real
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - Carmen González-Bosch
- Department of Biochemistry and Molecular Biology, University of Valencia, Agrochemical and Food Technology Institute (CSIC), 46980 Paterna, Valencia, Spain; (Ó.C.-S.); (L.S.-G.)
- Correspondence: ; Tel.: +34-963900022
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105
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Posner DC, Lin H, Meigs JB, Kolaczyk ED, Dupuis J. Convex combination sequence kernel association test for rare-variant studies. Genet Epidemiol 2020; 44:352-367. [PMID: 32100372 DOI: 10.1002/gepi.22287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/17/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Abstract
We propose a novel variant set test for rare-variant association studies, which leverages multiple single-nucleotide variant (SNV) annotations. Our approach optimizes a convex combination of different sequence kernel association test (SKAT) statistics, where each statistic is constructed from a different annotation and combination weights are optimized through a multiple kernel learning algorithm. The combination test statistic is evaluated empirically through data splitting. In simulations, we find our method preserves type I error at α = 2.5 × 1 0 - 6 and has greater power than SKAT(-O) when SNV weights are not misspecified and sample sizes are large ( N ≥ 5 , 000 ). We utilize our method in the Framingham Heart Study (FHS) to identify SNV sets associated with fasting glucose. While we are unable to detect any genome-wide significant associations between fasting glucose and 4-kb windows of rare variants ( p < 1 0 - 7 ) in 6,419 FHS participants, our method identifies suggestive associations between fasting glucose and rare variants near ROCK2 ( p = 2.1 × 1 0 - 5 ) and within CPLX1 ( p = 5.3 × 1 0 - 5 ). These two genes were previously reported to be involved in obesity-mediated insulin resistance and glucose-induced insulin secretion by pancreatic beta-cells, respectively. These findings will need to be replicated in other cohorts and validated by functional genomic studies.
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Affiliation(s)
- Daniel C Posner
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Honghuang Lin
- National Heart Lung and Blood Institute's, Boston University's Framingham Heart Study, Framingham, Massachusetts.,Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - James B Meigs
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric D Kolaczyk
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts.,National Heart Lung and Blood Institute's, Boston University's Framingham Heart Study, Framingham, Massachusetts
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106
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Hait NC, Maiti A, Xu P, Qi Q, Kawaguchi T, Okano M, Takabe K, Yan L, Luo C. Regulation of hypoxia-inducible factor functions in the nucleus by sphingosine-1-phosphate. FASEB J 2020; 34:4293-4310. [PMID: 32017264 PMCID: PMC10112293 DOI: 10.1096/fj.201901734rr] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 12/14/2022]
Abstract
Sphingosine kinase 2 (SphK2) is known to phosphorylate the nuclear sphingolipid metabolite to generate sphingosine-1-phosphate (S1P). Nuclear S1P is involved in epigenetic regulation of gene expression; however, the underlying mechanisms are not well understood. In this work, we have identified the role of nuclear S1P and SphK2 in regulating hypoxia-responsive master transcription factors hypoxia-inducible factor (HIF)-1α/2α, and their functions in breast cancer, with a focus on triple-negative breast cancer (TNBC). We have shown SphK2 is associated with HIF-1α in protein complexes, and is enriched at the promoters of HIF target genes, including vascular endothelial growth factor (VEGF), where it enhances local histone H3 acetylation and transcription. S1P specifically binds to the PAS domains of HIF-1α. SphK2, and HIF-1α expression levels are elevated in metastatic estrogen receptor-positive (ER+) and TNBC clinical tissue specimens compared to healthy breast tissue samples. To determine if S1P formation in the nucleus by SphK2 is a key regulator of HIF functions, we found using a preclinical TNBC xenograft mouse model, and an existing selective SphK2 inhibitor K-145, that nuclear S1P, histone acetylation, HIF-1α expression, and TNBC tumor growth were all reduced in vivo. Our results suggest that S1P and SphK2 in the nucleus are linked to the regulation of HIF-1α/2α functions associated with breast cancer progression, and may provide potential therapeutic targets.
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Affiliation(s)
- Nitai C Hait
- Division of Breast Surgery and Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Molecular & Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Aparna Maiti
- Division of Breast Surgery and Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Molecular & Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Pan Xu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Qianya Qi
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Tsutomu Kawaguchi
- Division of Breast Surgery and Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Maiko Okano
- Division of Breast Surgery and Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Kazuaki Takabe
- Division of Breast Surgery and Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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107
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Salinas RD, Connolly DR, Song H. Invited Review: Epigenetics in neurodevelopment. Neuropathol Appl Neurobiol 2020; 46:6-27. [PMID: 32056273 PMCID: PMC7174139 DOI: 10.1111/nan.12608] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/21/2020] [Accepted: 02/11/2020] [Indexed: 12/14/2022]
Abstract
Neural development requires the orchestration of dynamic changes in gene expression to regulate cell fate decisions. This regulation is heavily influenced by epigenetics, heritable changes in gene expression not directly explained by genomic information alone. An understanding of the complexity of epigenetic regulation is rapidly emerging through the development of novel technologies that can assay various features of epigenetics and gene regulation. Here, we provide a broad overview of several commonly investigated modes of epigenetic regulation, including DNA methylation, histone modifications, noncoding RNAs, as well as epitranscriptomics that describe modifications of RNA, in neurodevelopment and diseases. Rather than functioning in isolation, it is being increasingly appreciated that these various modes of gene regulation are dynamically interactive and coordinate the complex nature of neurodevelopment along multiple axes. Future work investigating these interactions will likely utilize 'multi-omic' strategies that assay cell fate dynamics in a high-dimensional and high-throughput fashion. Novel human neurodevelopmental models including iPSC and cerebral organoid systems may provide further insight into human-specific features of neurodevelopment and diseases.
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Affiliation(s)
- Ryan D. Salinas
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel R. Connolly
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongjun Song
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Glioblastoma Translational Center of Excellence, The Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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108
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Sadat-Shirazi MS, Asgari P, Mahboubi S, Nouri Zadeh-Tehrani S, Ashabi G, Rohbani K, Sabzevari S, Soltani H, Khalifeh S, Zarrindast MR. Effect of morphine exposure on novel object memory of the offspring: The role of histone H3 and ΔFosB. Brain Res Bull 2020; 156:141-149. [PMID: 31958477 DOI: 10.1016/j.brainresbull.2020.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/19/2019] [Accepted: 01/14/2020] [Indexed: 01/09/2023]
Abstract
It has been demonstrated that alteration in histone acetylation in the regions of the brain involved in the reward which may have an important role in morphine addiction. It is well established that epigenetic changes prior to birth influence the function and development of the brain. The current study was designed to evaluate changes in novel object memory, histone acetylation and ΔFosB in the brain of the offspring of morphine-withdrawn parents. Male and female Wistar rats received morphine orally for 21 following days. After ten days of abstinent, they were prepared for mating. The male offspring of the first parturition were euthanized on postnatal days 5, 21, 30 and 60. The novel object recognition (NOR) test was performed on adult male offspring. The amount of acetylated histone H3 and ΔFosB were evaluated in the prefrontal cortex (PFC) and hippocampus using western blotting. Obtained results indicated that the discrimination index in the NOR test was decreased in the offspring of morphine-withdrawn parents as compared with morphine-naïve offspring. In addition, the level of acetylated histone H3 was decreased in the PFC and hippocampus in the offspring of morphine-withdrawn parents during lifetime (postnatal days 5, 21, 30 and 60). In the case of ΔFosB, it also decreased in these regions in the morphine-withdrawn offspring. These results demonstrated that parental morphine exposure affects NOR memory, and decreased the level of histone H3 acetylation and ΔFosB in the PFC and hippocampus. Taken together, the effect of morphine might be transmitted to the next generation even after stop consuming morphine.
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Affiliation(s)
| | - Pardis Asgari
- Iranian National Center for Addiction Studies, Tehran University of Medical Sciences, Tehran, Iran
| | - Sarah Mahboubi
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Ghorbangol Ashabi
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Kiyana Rohbani
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Saba Sabzevari
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Haniyeh Soltani
- Iranian National Center for Addiction Studies, Tehran University of Medical Sciences, Tehran, Iran
| | - Solmaz Khalifeh
- Cognitive and Neuroscience Research Center (CNRC), Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohammad-Reza Zarrindast
- Iranian National Center for Addiction Studies, Tehran University of Medical Sciences, Tehran, Iran; Cognitive and Neuroscience Research Center (CNRC), Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Endocrinology and Metabolism Research Institute, Tehran University of Medical Science, Tehran, Iran.
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109
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Bhowmick K, Tehlan A, Sunita, Sudhakar R, Kaur I, Sijwali PS, Krishnamachari A, Dhar SK. Plasmodium falciparum GCN5 acetyltransferase follows a novel proteolytic processing pathway that is essential for its function. J Cell Sci 2020; 133:jcs.236489. [PMID: 31862795 DOI: 10.1242/jcs.236489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/29/2019] [Indexed: 12/18/2022] Open
Abstract
The pathogenesis of human malarial parasite Plasmodium falciparum is interlinked with its timely control of gene expression during its complex life cycle. In this organism, gene expression is partially controlled through epigenetic mechanisms, the regulation of which is, hence, of paramount importance to the parasite. The P. falciparum (Pf)-GCN5 histone acetyltransferase (HAT), an essential enzyme, acetylates histone 3 and regulates global gene expression in the parasite. Here, we show the existence of a novel proteolytic processing for PfGCN5 that is crucial for its activity in vivo We find that a cysteine protease-like enzyme is required for the processing of PfGCN5 protein. Immunofluorescence and immuno-electron microscopy analysis suggest that the processing event occurs in the vicinity of the digestive vacuole of the parasite following its trafficking through the classical ER-Golgi secretory pathway, before it subsequently reaches the nucleus. Furthermore, blocking of PfGCN5 processing leads to the concomitant reduction of its occupancy at the gene promoters and a reduced H3K9 acetylation level at these promoters, highlighting the important correlation between the processing event and PfGCN5 activity. Altogether, our study reveals a unique processing event for a nuclear protein PfGCN5 with unforeseen role of a food vacuolar cysteine protease. This leads to a possibility of the development of new antimalarials against these targets.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Krishanu Bhowmick
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ankita Tehlan
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sunita
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Renu Sudhakar
- Centre for Cellular and Molecular Biology, Hyderabad, Telengana 500007, India
| | - Inderjeet Kaur
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Puran Singh Sijwali
- Centre for Cellular and Molecular Biology, Hyderabad, Telengana 500007, India
| | | | - Suman Kumar Dhar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
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110
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Wu J, Ma N, Johnston LJ, Ma X. Dietary Nutrients Mediate Intestinal Host Defense Peptide Expression. Adv Nutr 2020; 11:92-102. [PMID: 31204774 PMCID: PMC7442325 DOI: 10.1093/advances/nmz057] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/14/2019] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
The intestinal tract is the shared locus of intestinal epithelial cells, immune cells, nutrient digestion and absorption, and microbial survival. The gut in animals faces continuous challenges in communicating with the external environment. Threats from endogenous imbalance and exogenous feeds, especially pathogens, could trigger a disorder of homeostasis, leading to intestinal disease and even systematic disease risk. As a part of the intestinal protective barrier, endogenous host defense peptides (HDPs) play multiple beneficial physiological roles in the gut mucosa. Moreover, enhancing endogenous HDPs is being developed as a new strategy for resisting pathogens and commensal microbes, and to maintain intestinal health and reduce antibiotic use. In recent years, multiple nutrients such as branched-chain amino acids, SCFAs, lactose, zinc, and cholecalciferol (vitamin D3) have been reported to significantly increase HDP expression. Nutritional intervention has received more attention and is viewed as a promising means to defend against pathogenic infections and intestinal inflammation. The present review focuses on current discoveries surrounding HDP expression and nutritional regulation of mechanisms in the gut. Our aim is to provide a comprehensive overview, referable tactics, and novel opinions.
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Affiliation(s)
- Jianmin Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lee J Johnston
- Swine Nutrition and Production, West Central Research and Outreach Center, University of Minnesota, Morris, MN, USA
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Department of Internal Medicine, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
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111
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Reich S, Weinstein DC. Repression of Inappropriate Gene Expression in the Vertebrate Embryonic Ectoderm. Genes (Basel) 2019; 10:E895. [PMID: 31698780 PMCID: PMC6895975 DOI: 10.3390/genes10110895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 01/01/2023] Open
Abstract
During vertebrate embryogenesis, precise regulation of gene expression is crucial for proper cell fate determination. Much of what we know about vertebrate development has been gleaned from experiments performed on embryos of the amphibian Xenopus laevis; this review will focus primarily on studies of this model organism. An early critical step during vertebrate development is the formation of the three primary germ layers-ectoderm, mesoderm, and endoderm-which emerge during the process of gastrulation. While much attention has been focused on the induction of mesoderm and endoderm, it has become clear that differentiation of the ectoderm involves more than the simple absence of inductive cues; rather, it additionally requires the inhibition of mesendoderm-promoting genes. This review aims to summarize our current understanding of the various inhibitors of inappropriate gene expression in the presumptive ectoderm.
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Affiliation(s)
- Shoshana Reich
- PhD Program in Biology, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Daniel C. Weinstein
- PhD Program in Biology, The Graduate Center, The City University of New York, New York, NY 10016, USA
- Department of Biology, Queens College, The City University of New York, Queens, NY 11367, USA
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112
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Tao H, Li Q, Lin Y, Zuo H, Cui Y, Chen S, Chen Z, Liu H. Coordinated expression of p300 and HDAC3 upregulates histone acetylation during dentinogenesis. J Cell Biochem 2019; 121:2478-2488. [PMID: 31692090 DOI: 10.1002/jcb.29470] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 10/08/2019] [Indexed: 02/06/2023]
Abstract
Cellular differentiation is caused by highly controlled modifications in the gene expression but rarely involves a change in the DNA sequence itself. Histone acetylation is a major epigenetic factor that adds an acetyl group to histone proteins, thus altering their interaction with DNA and nuclear proteins. Illumination of the histone acetylation during dentinogenesis is important for odontoblast differentiation and dentinogenesis. In the current study, we aimed to discover the roles and regulation of acetylation at histone 3 lysine 9 (H3K9ac) and H3K27ac during dentinogenesis. We first found that both of these modifications were enhanced during odontoblast differentiation and dentinogenesis. These modifications are dynamically catalyzed by histone acetyltransferases (HATs) and deacetylases (HDACs), among which HDAC3 was decreased while p300 increased during odontoblast differentiation. Moreover, overexpression of HDAC3 or knockdown p300 inhibited odontoblast differentiation in vitro, and inhibition of HDAC3 and p300 with trichostatin A or C646 regulated odontoblast differentiation. Taken together, the results of our present study suggest that histone acetylation is involved in dentinogenesis and coordinated expression of p300- and HDAC3-regulated odontoblast differentiation through upregulating histone acetylation.
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Affiliation(s)
- Huangheng Tao
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Qiuhui Li
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yuxiu Lin
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Huanyan Zuo
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yu Cui
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Shuo Chen
- Department of Developmental Dentistry, University of Texas Health Science Center, San Antonio, Texas
| | - Zhi Chen
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Huan Liu
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Periodontology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
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113
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Paternal valproic acid exposure in mice triggers behavioral alterations in offspring. Neurotoxicol Teratol 2019; 76:106837. [DOI: 10.1016/j.ntt.2019.106837] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/22/2019] [Accepted: 09/18/2019] [Indexed: 01/29/2023]
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114
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Cencioni C, Heid J, Krepelova A, Rasa SMM, Kuenne C, Guenther S, Baumgart M, Cellerino A, Neri F, Spallotta F, Gaetano C. Aging Triggers H3K27 Trimethylation Hoarding in the Chromatin of Nothobranchius furzeri Skeletal Muscle. Cells 2019; 8:cells8101169. [PMID: 31569376 PMCID: PMC6829443 DOI: 10.3390/cells8101169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/15/2019] [Accepted: 09/26/2019] [Indexed: 01/10/2023] Open
Abstract
Aging associates with progressive loss of skeletal muscle function, sometimes leading to sarcopenia, a process characterized by impaired mobility and weakening of muscle strength. Since aging associates with profound epigenetic changes, epigenetic landscape alteration analysis in the skeletal muscle promises to highlight molecular mechanisms of age-associated alteration in skeletal muscle. This study was conducted exploiting the short-lived turquoise killifish Nothobranchius furzeri (Nfu), a relatively new model for aging studies. The epigenetic analysis suggested a less accessible and more condensed chromatin in old Nfu skeletal muscle. Specifically, an accumulation of heterochromatin regions was observed as a consequence of increased levels of H3K27me3, HP1α, polycomb complex subunits, and senescence-associated heterochromatic foci (SAHFs). Consistently, euchromatin histone marks, including H3K9ac, were significantly reduced. In this context, integrated bioinformatics analysis of RNASeq and ChIPSeq, related to skeletal muscle of Nfu at different ages, revealed a down-modulation of genes involved in cell cycle, differentiation, and DNA repair and an up-regulation of inflammation and senescence genes. Undoubtedly, more studies are needed to disclose the detailed mechanisms; however, our approach enlightened unprecedented features of Nfu skeletal muscle aging, potentially associated with swimming impairment and reduced mobility typical of old Nfu.
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Affiliation(s)
- Chiara Cencioni
- National Research Council, Institute for Systems Analysis and Computer Science, 00185 Rome, Italy.
| | - Johanna Heid
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Anna Krepelova
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
| | | | - Carsten Kuenne
- ECCPS Bioinformatics and deep sequencing platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany.
| | - Stefan Guenther
- ECCPS Bioinformatics and deep sequencing platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany.
| | - Mario Baumgart
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
| | - Alessandro Cellerino
- Laboratory of Biology (Bio@SNS), Scuola Normale Superiore, c/o Istituto di Biofisica del CNR, 56124 Pisa, Italy.
| | - Francesco Neri
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany.
| | - Francesco Spallotta
- Department of Oncology, University of Turin, 10060 Candiolo (TO), Italy.
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (TO), Italy.
| | - Carlo Gaetano
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy.
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115
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Lin R, Luo L, Gong Y, Zheng J, Wang S, Du J, Luo D. Immunohistochemical analysis of histone H3 acetylation in the trigeminal root entry zone in an animal model of trigeminal neuralgia. J Neurosurg 2019; 131:828-838. [PMID: 30497181 DOI: 10.3171/2018.5.jns172948] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/23/2018] [Indexed: 01/13/2023]
Abstract
OBJECTIVE The trigeminal root entry zone (TREZ) is a transitional zone between the central nervous system (CNS) and peripheral nervous system (PNS), adjacent to the brainstem. Microvascular compression of the TREZ has been considered to be the primary etiology in most cases of trigeminal neuralgia (TN), but whether epigenetic regulation is involved in the pathogenesis of TN is still unclear. Therefore, this study was designed to investigate the epigenetic regulation of histone H3 acetylation in the TREZ in an animal model of TN. METHODS An animal model of TN was established, and adult male Sprague-Dawley rats were randomly assigned to a TN group with trigeminal nerve root compression, sham operation group, TN+HDACi group (TN plus selective histone deacetylase inhibitor injection into the TREZ), or TN+Veh group (TN plus vehicle injection into the TREZ). To measure the length of the central portion of the TREZ from the junction of the trigeminal nerve root entering the pons to the interface of the dome-shaped CNS-PNS transitional zone, immunofluorescent staining of glia and glial nuclei was performed using glial fibrillary acidic protein (GFAP) antibody and DAPI, respectively. To investigate the acetylation of histone H3 within the TREZ in a TN animal model group and a sham operation group, localization of histone H3K9, H3K18, and H3K27 acetylation was examined via immunohistochemical staining methods. RESULTS Measurements of the CNS-PNS transitional zone in the TREZ revealed that the average length from the junction of the trigeminal nerve root connecting the pons to the glial fringe of the TREZ in the TN group was longer than that in the sham operation group (p < 0.05) and that the interface gradually migrated distally. Cells that stained positive for acetylated histone H3K9, H3K18, and H3K27 were distributed around both sides of the border of the CNS-PNS junction in the TREZ. The ratio of immunoreactive H3K9-, H3K18- and H3K27-positive cells in the TN group was obviously higher than that in the sham operation group on postoperative days 7, 14, 21, and 28 (p < 0.05). CONCLUSIONS These results suggested that chronic compression of the trigeminal nerve root may be involved in the pathogenesis of TN in an animal model by influencing the plasticity of the CNS-PNS transitional zone and the level of histone acetylation in the TREZ.
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Affiliation(s)
- Ren Lin
- 1Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University
- 3Key Laboratory of Brain Aging and Neurodegenerative Diseases of Fujian Province, Fuzhou, Fujian, People's Republic of China
| | - Lili Luo
- 1Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University
| | - Yiran Gong
- 1Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University
| | - Jingsheng Zheng
- 1Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University
| | - Shuiyue Wang
- 1Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University
| | - Junjie Du
- 1Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University
| | - Daoshu Luo
- 1Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University
- 2Fujian Provincial Key Laboratory of Neuroglia and Disease; and
- 3Key Laboratory of Brain Aging and Neurodegenerative Diseases of Fujian Province, Fuzhou, Fujian, People's Republic of China
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116
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Chen FX, Smith ER, Shilatifard A. Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2019; 19:464-478. [PMID: 29740129 DOI: 10.1038/s41580-018-0010-5] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The dynamic regulation of transcription elongation by RNA polymerase II (Pol II) is an integral part of the implementation of gene expression programmes during development. In most metazoans, the majority of transcribed genes exhibit transient pausing of Pol II at promoter-proximal regions, and the release of Pol II into gene bodies is controlled by many regulatory factors that respond to environmental and developmental cues. Misregulation of the elongation stage of transcription is implicated in cancer and other human diseases, suggesting that mechanistic understanding of transcription elongation control is therapeutically relevant. In this Review, we discuss the features, establishment and maintenance of Pol II pausing, the transition into productive elongation, the control of transcription elongation by enhancers and by factors of other cellular processes, such as topoisomerases and poly(ADP-ribose) polymerases (PARPs), and the potential of therapeutic targeting of the elongation stage of transcription by Pol II.
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Affiliation(s)
- Fei Xavier Chen
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Edwin R Smith
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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117
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Chen J, Sagum C, Bedford MT. Protein domain microarrays as a platform to decipher signaling pathways and the histone code. Methods 2019; 184:4-12. [PMID: 31449908 DOI: 10.1016/j.ymeth.2019.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 01/07/2023] Open
Abstract
Signal transduction is driven by protein interactions that are controlled by posttranslational modifications (PTM). Usually, protein domains are responsible for "reading" the PTM signal deposited on the interacting partners. Protein domain microarrays have been developed as a high throughput platform to facilitate the rapid identification of protein-protein interactions, and this approach has become broadly used in biomedical research. In this review, we will summarize the history, development and applications of this technique, including the use of protein domain microarrays in identifying both novel protein-protein interactions and small molecules that block these interactions. We will focus on the approaches we use in the Protein Array and Analysis Core - the PAAC - at MD Anderson Cancer Center. We will also address the technical limitations and discuss future directions.
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Affiliation(s)
- Jianji Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Cari Sagum
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
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118
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Etchegaray JP, Zhong L, Li C, Henriques T, Ablondi E, Nakadai T, Van Rechem C, Ferrer C, Ross KN, Choi JE, Samarakkody A, Ji F, Chang A, Sadreyev RI, Ramaswamy S, Nechaev S, Whetstine JR, Roeder RG, Adelman K, Goren A, Mostoslavsky R. The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing. Mol Cell 2019; 75:683-699.e7. [PMID: 31399344 PMCID: PMC6907403 DOI: 10.1016/j.molcel.2019.06.034] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/11/2019] [Accepted: 06/24/2019] [Indexed: 12/19/2022]
Abstract
Transcriptional regulation in eukaryotes occurs at promoter-proximal regions wherein transcriptionally engaged RNA polymerase II (Pol II) pauses before proceeding toward productive elongation. The role of chromatin in pausing remains poorly understood. Here, we demonstrate that the histone deacetylase SIRT6 binds to Pol II and prevents the release of the negative elongation factor (NELF), thus stabilizing Pol II promoter-proximal pausing. Genetic depletion of SIRT6 or its chromatin deficiency upon glucose deprivation causes intragenic enrichment of acetylated histone H3 at lysines 9 (H3K9ac) and 56 (H3K56ac), activation of cyclin-dependent kinase 9 (CDK9)-that phosphorylates NELF and the carboxyl terminal domain of Pol II-and enrichment of the positive transcription elongation factors MYC, BRD4, PAF1, and the super elongation factors AFF4 and ELL2. These events lead to increased expression of genes involved in metabolism, protein synthesis, and embryonic development. Our results identified SIRT6 as a Pol II promoter-proximal pausing-dedicated histone deacetylase.
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Affiliation(s)
- Jean-Pierre Etchegaray
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA.
| | - Lei Zhong
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Catherine Li
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eileen Ablondi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Capucine Van Rechem
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Christina Ferrer
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Kenneth N Ross
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Jee-Eun Choi
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Ann Samarakkody
- University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew Chang
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Sridhar Ramaswamy
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Sergei Nechaev
- University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
| | - Johnathan R Whetstine
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Alon Goren
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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119
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Al Sayed R, Smith W, Rogers N, Smith N, Clark D, Castillo G, McLeod H, Glenister S, Shorter KR. A 2x folic acid treatment affects epigenetics and dendritic spine densities in SHSY5Y cells. Biochem Biophys Rep 2019; 20:100681. [PMID: 31467993 PMCID: PMC6711848 DOI: 10.1016/j.bbrep.2019.100681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/20/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022] Open
Abstract
Many diseases are now associated with aberrant epigenetics and gene expression changes. Epigenetics can be modified by factors like diet. One dietary factor, folic acid, is consumed in various forms including supplements, energy drinks, and fortified grains. It was hypothesized high levels of folic acid would affect gene expression and enzyme activity of chromatin modifying enzymes as well as dendritic spine densities in a commonly utilized neuron model, the SHSY5Y cell. Decreased MBD2 and MECP2 were discovered upon treatment of SHSY5Y cells with a 2x folic acid dose. Corresponding decreases in dendritic spines were apparent in the 2x folic acid treated cells as well. Activity of DNMTs and H3K4 HMTs was altered. Further, H3K4me1, H3K4me3, H3K9Ac, and global DNA methylation were decreased in the 2x folic acid treated cells. Further studies are warranted to determine if the effects of excess folic acid are detrimental to organismal physiology. The 2x folic acid treatment in SHSY5Y cells induces a significant decrease in MBD2 and MECP2 mRNA expression. The excess folic acid also causes a significant increase in dendritic spines in SHSY5Y cells. The 2x folic acid treatment increases DNMT activity and significantly decreases H3K4 HMT activity in SHSY5Y cells. These findings align with some of those seen in autism spectrum disorders.
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Affiliation(s)
- Rahaf Al Sayed
- University of South Carolina Upstate Division of Natural Sciences and Engineering, 800 University Way, Spartanburg, SC, 29303, USA
| | - Whitnei Smith
- University of South Carolina Upstate Division of Natural Sciences and Engineering, 800 University Way, Spartanburg, SC, 29303, USA
| | - Nicole Rogers
- University of South Carolina Upstate Division of Natural Sciences and Engineering, 800 University Way, Spartanburg, SC, 29303, USA
| | - Nuri Smith
- University of South Carolina Upstate Division of Natural Sciences and Engineering, 800 University Way, Spartanburg, SC, 29303, USA
| | - Daniel Clark
- University of South Carolina Upstate Division of Natural Sciences and Engineering, 800 University Way, Spartanburg, SC, 29303, USA
| | - Gabriel Castillo
- University of South Carolina Upstate Division of Natural Sciences and Engineering, 800 University Way, Spartanburg, SC, 29303, USA
| | - Hunter McLeod
- University of South Carolina Upstate Division of Natural Sciences and Engineering, 800 University Way, Spartanburg, SC, 29303, USA
| | - Stewart Glenister
- University of South Carolina Upstate Division of Natural Sciences and Engineering, 800 University Way, Spartanburg, SC, 29303, USA
| | - Kimberly R Shorter
- University of South Carolina Upstate Division of Natural Sciences and Engineering, 800 University Way, Spartanburg, SC, 29303, USA
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120
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Cobos SN, Bennett SA, Torrente MP. The impact of histone post-translational modifications in neurodegenerative diseases. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1982-1991. [PMID: 30352259 PMCID: PMC6475498 DOI: 10.1016/j.bbadis.2018.10.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/05/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023]
Abstract
Every year, neurodegenerative disorders take more than 5000 lives in the US alone. Cures have not yet been found for many of the multitude of neuropathies. The majority of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and Parkinson's disease (PD) cases have no known genetic basis. Thus, it is evident that contemporary genetic approaches have failed to explain the etiology or etiologies of ALS/FTD and PD. Recent investigations have explored the potential role of epigenetic mechanisms in disease development. Epigenetics comprises heritable changes in gene utilization that are not derived from changes in the genome. A main epigenetic mechanism involves the post-translational modification of histones. Increased knowledge of the epigenomic landscape of neurodegenerative diseases would not only further our understanding of the disease pathologies, but also lead to the development of treatments able to halt their progress. Here, we review recent advances on the association of histone post-translational modifications with ALS, FTD, PD and several ataxias.
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Affiliation(s)
- Samantha N Cobos
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States; Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Seth A Bennett
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Mariana P Torrente
- Chemistry Department of Brooklyn College, Brooklyn, New York 11210, United States; Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York 10016, United States.
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121
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Histone deacetylase inhibitors promote ATP2A3 gene expression in hepatocellular carcinoma cells: p300 as a transcriptional regulator. Int J Biochem Cell Biol 2019; 113:8-16. [DOI: 10.1016/j.biocel.2019.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/22/2019] [Accepted: 05/25/2019] [Indexed: 11/24/2022]
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122
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Arndt DL, Wukitsch TJ, Garcia EJ, Cain M. Histone deacetylase inhibition differentially attenuates cue-induced reinstatement: An interaction of environment and acH3K9 expression in the dorsal striatum. Behav Neurosci 2019; 133:478-488. [PMID: 31343201 DOI: 10.1037/bne0000333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Substance use disorder is driven by complex gene-environment interactions. Epigenetic histone regulation is a significant contributor to several behavioral phenotypes of drug abuse. The primary epigenetic mechanisms that drive drug taking and drug seeking are still being investigated, and it is unclear how environmental conditions alter epigenetic histone acetylation to change behaviors geared toward drug reward. This study examined the effects of environmental condition on amphetamine self-administration, and whether drug-taking and drug-seeking behaviors could be influenced through inhibition of an epigenetic regulator, histone deacetylase (HDAC). Male rats reared for 30 days in enriched (EC), isolated (IC), or standard conditions (SC) prior to amphetamine (0.03, 0.05, 0.1 mg/kg/infusion, IV) self-administration, extinction, and reinstatement sessions. The HDAC inhibitor, Trichostatin A (TsA; 0.3 mg/kg, IV), was injected 30 min prior to operant sessions. After amphetamine-induced reinstatement (0.25 mg/kg, subcutaneous [s.c.]), tissue was extracted for Western blot analyses of acetylated histone H3 lysine 9 (acH3K9) in the nucleus accumbens (NAc) and dorsal striatum (DSt). While TsA did not significantly affect amphetamine self-administration or extinction, TsA decreased cue-, but not drug-induced reinstatement in IC rats only. In the DSt, but not in the NAc, IC rats exhibited significantly less acH3K9 expression than EC and SC rats, irrespective of TsA treatment. HDAC inhibition decreases cue-induced reinstatement of amphetamine seeking in IC rats. While IC rats exhibit less acH3K9 expression in the DSt, future studies are needed to elucidate the critical epigenetic factors that drive substance abuse, particularly in vulnerable populations. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
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Affiliation(s)
| | | | | | - Mary Cain
- Department of Psychological Sciences
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123
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Master control: transcriptional regulation of mammalian Myod. J Muscle Res Cell Motil 2019; 40:211-226. [PMID: 31301002 PMCID: PMC6726840 DOI: 10.1007/s10974-019-09538-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/03/2019] [Indexed: 12/22/2022]
Abstract
MYOD is a master regulator of the skeletal myogenic program. But what regulates expression of Myod? More than 20 years ago, studies established that Myod expression is largely controlled by just two enhancer regions located within a region 24 kb upstream of the transcription start site in mammals, which regulate Myod expression in the embryo, fetus and adult. Despite this apparently simple arrangement, Myod regulation is complex, with different combinations of transcription factors acting on these enhancers in different muscle progenitor cells and phases of differentiation. A range of epigenetic modifications in the Myod upstream region also play a part in activating and repressing Myod expression during development and regeneration. Here the evidence for this binding at Myod control regions is summarized, giving an overview of our current understanding of Myod expression regulation in mammals.
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124
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Riedlinger T, Bartkuhn M, Zimmermann T, Hake SB, Nist A, Stiewe T, Kracht M, Schmitz ML. Chemotherapeutic Drugs Inhibiting Topoisomerase 1 Activity Impede Cytokine-Induced and NF-κB p65-Regulated Gene Expression. Cancers (Basel) 2019; 11:cancers11060883. [PMID: 31242600 PMCID: PMC6627772 DOI: 10.3390/cancers11060883] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 02/03/2023] Open
Abstract
Inhibitors of DNA topoisomerase I (TOP1), an enzyme relieving torsional stress of DNA by generating transient single-strand breaks, are clinically used to treat ovarian, small cell lung and cervical cancer. As torsional stress is generated during transcription by progression of RNA polymerase II through the transcribed gene, we tested the effects of camptothecin and of the approved TOP1 inhibitors Topotecan and SN-38 on TNFα-induced gene expression. RNA-seq experiments showed that inhibition of TOP1 but not of TOP2 activity suppressed the vast majority of TNFα-triggered genes. The TOP1 effects were fully reversible and preferentially affected long genes. TNFα stimulation led to inducible recruitment of TOP1 to the gene body of IL8, where its inhibition by camptothecin reduced transcription elongation and also led to altered histone H3 acetylation. Together, these data show that TOP1 inhibitors potently suppress expression of proinflammatory cytokines, a feature that may contribute to the increased infection risk occurring in tumor patients treated with these agents. On the other hand, TOP1 inhibitors could also be considered as a therapeutic option in order to interfere with exaggerated cytokine expression seen in several inflammatory diseases.
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Affiliation(s)
- Tabea Riedlinger
- Institute of Biochemistry, Justus Liebig University, D-35392 Giessen, Germany.
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany.
| | - Tobias Zimmermann
- Bioinformatics and Systems Biology, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany.
| | - Andrea Nist
- Genomics Core Facility and Institute of Molecular Oncology, Philipps University Marburg, D-35043 Marburg, Germany.
| | - Thorsten Stiewe
- Genomics Core Facility and Institute of Molecular Oncology, Philipps University Marburg, D-35043 Marburg, Germany.
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Justus Liebig University, D-35392 Giessen, Germany.
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus Liebig University, D-35392 Giessen, Germany.
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125
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Akmammedov A, Geigges M, Paro R. Bivalency in Drosophila embryos is associated with strong inducibility of Polycomb target genes. Fly (Austin) 2019; 13:42-50. [PMID: 31094269 DOI: 10.1080/19336934.2019.1619438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins orchestrate development of a multicellular organism by faithfully maintaining cell fate decisions made early in embryogenesis. An important chromatin mark connected to PcG/TrxG regulation is bivalent domains, the simultaneous presence of H3K27me3 and H3K4me3 on a given locus, originally identified in mammalian embryonic stem cells but considered to be absent in invertebrates. Here, we provide evidence for the existence of bivalency in fly embryos. Using a recently described PcG reporter fly line, we observed a strong reporter inducibility in the embryo and its sharp decrease in larval and adult stages. Analysis of the chromatin landscape of the reporter revealed a strong signal for the repressive PcG mark, H3K27me3, in all three developmental stages and, surprisingly, a strong signal for a transcriptionally activating H3K4me3 mark in the embryo. Using re-chromatin immunoprecipitation experiments, bivalent domains were also uncovered at endogenous PcG targets like the Hox genes.
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Affiliation(s)
- Arslan Akmammedov
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Marco Geigges
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
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126
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Gottesfeld JM. Milestones in transcription and chromatin published in the Journal of Biological Chemistry. J Biol Chem 2019; 294:1652-1660. [PMID: 30710013 DOI: 10.1074/jbc.tm118.004162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
During Herbert Tabor's tenure as Editor-in-Chief from 1971 to 2010, JBC has published many seminal papers in the fields of chromatin structure, epigenetics, and regulation of transcription in eukaryotes. As of this writing, more than 21,000 studies on gene transcription at the molecular level have been published in JBC since 1971. This brief review will attempt to highlight some of these ground-breaking discoveries and show how early studies published in JBC have influenced current research. Papers published in the Journal have reported the initial discovery of multiple forms of RNA polymerase in eukaryotes, identification and purification of essential components of the transcription machinery, and identification and mechanistic characterization of various transcriptional activators and repressors and include studies on chromatin structure and post-translational modifications of the histone proteins. The large body of literature published in the Journal has inspired current research on how chromatin organization and epigenetics impact regulation of gene expression.
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Affiliation(s)
- Joel M Gottesfeld
- Departments of Molecular Medicine and Chemistry, The Scripps Research Institute, La Jolla, California 92037.
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127
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Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription. Essays Biochem 2019; 63:97-107. [PMID: 30940741 PMCID: PMC6484784 DOI: 10.1042/ebc20180061] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
Packaging the long and fragile genomes of eukaryotic species into nucleosomes is all well and good, but how do cells gain access to the DNA again after it has been bundled away? The solution, in every species from yeast to man, is to post-translationally modify histones, altering their chemical properties to either relax the chromatin, label it for remodelling or make it more compact still. Histones are subject to a myriad of modifications: acetylation, methylation, phosphorylation, ubiquitination etc. This review focuses on histone acylations, a diverse group of modifications which occur on the ε-amino group of Lysine residues and includes the well-characterised Lysine acetylation. Over the last 50 years, histone acetylation has been extensively characterised, with the discovery of histone acetyltransferases (HATs) and histone deacetylases (HDACs), and global mapping experiments, revealing an association of hyperacetylated histones with accessible, transcriptionally active chromatin. More recently, there has been an explosion in the number of unique short chain ‘acylations’ identified by MS, including: propionylation, butyrylation, crotonylation, succinylation, malonylation and 2-hydroxyisobutyrylation. These novel modifications add a range of chemical environments to histones, and similar to acetylation, appear to accumulate at transcriptional start sites and correlate with gene activity.
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128
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Rajendran P, Johnson G, Li L, Chen YS, Dashwood M, Nguyen N, Ulusan A, Ertem F, Zhang M, Li J, Sun D, Huang Y, Wang S, Leung HC, Lieberman D, Beaver L, Ho E, Bedford M, Chang K, Vilar E, Dashwood R. Acetylation of CCAR2 Establishes a BET/BRD9 Acetyl Switch in Response to Combined Deacetylase and Bromodomain Inhibition. Cancer Res 2019; 79:918-927. [PMID: 30643017 DOI: 10.1158/0008-5472.can-18-2003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/19/2018] [Accepted: 01/09/2019] [Indexed: 12/15/2022]
Abstract
There continues to be interest in targeting epigenetic "readers, writers, and erasers" for the treatment of cancer and other pathologies. However, a mechanistic understanding is frequently lacking for the synergy observed when combining deacetylase and bromodomain inhibitors. Here we identify cell cycle and apoptosis regulator 2 (CCAR2) as an early target for acetylation in colon cancer cells treated with sulforaphane. N-terminal acetylation of CCAR2 diminished its interactions with histone deacetylase 3 and β-catenin, interfering with Wnt coactivator functions of CCAR2, including in cells harboring genetically encoded CCAR2 acetylation. Protein domain arrays and pull-down assays identified acetyl "reader" proteins that recognized CCAR2 acetylation sites, including BRD9 and members of the bromodomain and extraterminal domain (BET) family. Treatment with the BET inhibitor JQ1 synergized with sulforaphane in colon cancer cells and suppressed tumor development effectively in a preclinical model of colorectal cancer. Studies with sulforaphane+JQ1 in combination implicated a BET/BRD9 acetyl switch and a shift in the pool of acetyl "reader" proteins in favor of BRD9-regulated target genes. SIGNIFICANCE: These results highlight the competition that exists among the "readers" of acetylated histone and nonhistone proteins and provide a mechanistic basis for potential new therapeutic avenues involving epigenetic combination treatments.
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Affiliation(s)
- Praveen Rajendran
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas.
| | - Gavin Johnson
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Li Li
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Ying-Shiuan Chen
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Mohaiza Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Nhung Nguyen
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Ahmet Ulusan
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Furkan Ertem
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Mutian Zhang
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Deqiang Sun
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Shan Wang
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Hon-Chiu Leung
- Mass Spectrometry-Proteomics Core, Baylor College of Medicine, Houston, Texas
| | - David Lieberman
- Division of Gastroenterology and Hepatology, Oregon Health & Science University, Portland, Oregon
| | - Laura Beaver
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon
| | - Emily Ho
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon
| | - Mark Bedford
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle Chang
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eduardo Vilar
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roderick Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas. .,The University of Texas MD Anderson Cancer Center, Houston, Texas
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129
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Song W, Ovcharenko I. Dichotomy in redundant enhancers points to presence of initiators of gene regulation. BMC Genomics 2018; 19:947. [PMID: 30563465 PMCID: PMC6299655 DOI: 10.1186/s12864-018-5335-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022] Open
Abstract
Background The regulatory landscape of a gene locus often consists of several functionally redundant enhancers establishing phenotypic robustness and evolutionary stability of its regulatory program. However, it is unclear what mechanisms are employed by redundant enhancers to cooperatively orchestrate gene expression. Results By comparing redundant enhancers to single enhancers (enhancers present in a single copy in a gene locus), we observed that the DNA sequence encryption differs between these two classes of enhancers, suggesting a difference in their regulatory mechanisms. Initiator enhancers, which are a subset of redundant enhancers and show similar sequence encryption to single enhancers, differ from the rest of redundant enhancers in their sequence encryption, evolutionary conservation and proximity to target genes. Genes hosting initiator enhancers in their loci feature elevated levels of expression. Initiator enhancers show a high level of 3D chromatin contacts with both transcription start sites and regular enhancers, suggesting their roles as primary activators and intermediate catalysts of gene expression, through which the regulatory signals of redundant enhancers are propagated to the target genes. In addition, GWAS and eQTLs variants are significantly enriched in initiator enhancers compared to redundant enhancers, suggesting a key functional role these sequences play in gene regulation. Conclusions The specific characteristics and widespread abundance of initiator enhancers advocate for a possible universal hierarchical mechanism of tissue-specific gene regulation involving multiple redundant enhancers acting through initiator enhancers. Electronic supplementary material The online version of this article (10.1186/s12864-018-5335-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Song
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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130
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Sen R, Pezoa SA, Carpio Shull L, Hernandez-Lagunas L, Niswander LA, Artinger KB. Kat2a and Kat2b Acetyltransferase Activity Regulates Craniofacial Cartilage and Bone Differentiation in Zebrafish and Mice. J Dev Biol 2018; 6:jdb6040027. [PMID: 30424580 PMCID: PMC6315545 DOI: 10.3390/jdb6040027] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/26/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022] Open
Abstract
Cranial neural crest cells undergo cellular growth, patterning, and differentiation within the branchial arches to form cartilage and bone, resulting in a precise pattern of skeletal elements forming the craniofacial skeleton. However, it is unclear how cranial neural crest cells are regulated to give rise to the different shapes and sizes of the bone and cartilage. Epigenetic regulators are good candidates to be involved in this regulation, since they can exert both broad as well as precise control on pattern formation. Here, we investigated the role of the histone acetyltransferases Kat2a and Kat2b in craniofacial development using TALEN/CRISPR/Cas9 mutagenesis in zebrafish and the Kat2ahat/hat (also called Gcn5) allele in mice. kat2a and kat2b are broadly expressed during embryogenesis within the central nervous system and craniofacial region. Single and double kat2a and kat2b zebrafish mutants have an overall shortening and hypoplastic nature of the cartilage elements and disruption of the posterior ceratobranchial cartilages, likely due to smaller domains of expression of both cartilage- and bone-specific markers, including sox9a and col2a1, and runx2a and runx2b, respectively. Similarly, in mice we observe defects in the craniofacial skeleton, including hypoplastic bone and cartilage and altered expression of Runx2 and cartilage markers (Sox9, Col2a1). In addition, we determined that following the loss of Kat2a activity, overall histone 3 lysine 9 (H3K9) acetylation, the main epigenetic target of Kat2a/Kat2b, was decreased. These results suggest that Kat2a and Kat2b are required for growth and differentiation of craniofacial cartilage and bone in both zebrafish and mice by regulating H3K9 acetylation.
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Affiliation(s)
- Rwik Sen
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Sofia A Pezoa
- Cell Biology, Stem Cells, and Development Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
- Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Lomeli Carpio Shull
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Laura Hernandez-Lagunas
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Lee A Niswander
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
- Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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131
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López C, Aguilar R, Nardocci G, Cereceda K, Vander Stelt K, Slebe JC, Montecino M, Concha II. Wnt/β-catenin signaling enhances transcription of the CX43 gene in murine Sertoli cells. J Cell Biochem 2018; 120:6753-6762. [PMID: 30417410 DOI: 10.1002/jcb.27973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 10/02/2018] [Indexed: 01/12/2023]
Abstract
Sertoli cells provide the nutritional and metabolic support for germ cells. Wnt/β-catenin signaling is important for the development of the seminiferous epithelium during embryonic age, although after birth this pathway is downregulated. Cx43 gene codes for a protein that is critical during testicular development. The Cx43 promoter contains TCF/β-catenin binding elements (TBEs) that contribute CX43 expression in different cell types and which may also be regulating the expression of this gene in Sertoli cells. In this study, we demonstrate that 42GPA9 Sertoli cells respond to treatments that result in accumulation of β-catenin within the nucleus and in upregulation of CX43 gene transcription. β-Catenin binds to TBEs located both upstream and downstream of the transcriptional start site (TSS). Luciferase reporter experiments revealed that TBEs located upstream of the TSS are necessary for β-catenin-mediated upregulation. Our results also indicate that the Wnt/β-catenin-dependent upregulation of the Cx43 gene in Sertoli cells is accompanied by changes in epigenetic parameters that may be directly contributing to generating a chromatin environment that facilitates the establishment of the transcriptional machinery at this promoter.
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Affiliation(s)
- Camila López
- Instituto de Bioquimíca y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Rodrigo Aguilar
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
| | - Gino Nardocci
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
| | - Karina Cereceda
- Instituto de Bioquimíca y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Karen Vander Stelt
- Instituto de Bioquimíca y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Juan Carlos Slebe
- Instituto de Bioquimíca y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Martin Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
| | - Ilona I Concha
- Instituto de Bioquimíca y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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132
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Li X, Li XM, Jiang Y, Liu Z, Cui Y, Fung KY, van der Beelen SHE, Tian G, Wan L, Shi X, Allis CD, Li H, Li Y, Li XD. Structure-guided development of YEATS domain inhibitors by targeting π-π-π stacking. Nat Chem Biol 2018; 14:1140-1149. [PMID: 30374167 DOI: 10.1038/s41589-018-0144-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/31/2018] [Indexed: 01/08/2023]
Abstract
Chemical probes of epigenetic 'readers' of histone post-translational modifications (PTMs) have become powerful tools for mechanistic and functional studies of their target proteins in normal physiology and disease pathogenesis. Here we report the development of the first class of chemical probes of YEATS domains, newly identified 'readers' of histone lysine acetylation (Kac) and crotonylation (Kcr). Guided by the structural analysis of a YEATS-Kcr complex, we developed a series of peptide-based inhibitors of YEATS domains by targeting a unique π-π-π stacking interaction at the proteins' Kcr recognition site. Further structure optimization resulted in the selective inhibitors preferentially binding to individual YEATS-containing proteins including AF9 and ENL with submicromolar affinities. We demonstrate that one of the ENL YEATS-selective inhibitors, XL-13m, engages with endogenous ENL, perturbs the recruitment of ENL onto chromatin, and synergizes the BET and DOT1L inhibition-induced downregulation of oncogenes in MLL-rearranged acute leukemia.
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Affiliation(s)
- Xin Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yixiang Jiang
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yiwen Cui
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Ka Yi Fung
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | | | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Liling Wan
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C David Allis
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China. .,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China.
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133
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Zhang T, Wei G, Millard CJ, Fischer R, Konietzny R, Kessler BM, Schwabe JWR, Brockdorff N. A variant NuRD complex containing PWWP2A/B excludes MBD2/3 to regulate transcription at active genes. Nat Commun 2018; 9:3798. [PMID: 30228260 PMCID: PMC6143588 DOI: 10.1038/s41467-018-06235-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
Abstract
Transcriptional regulation by chromatin is a highly dynamic process directed through the recruitment and coordinated action of epigenetic modifiers and readers of these modifications. Using an unbiased proteomic approach to find interactors of H3K36me3, a modification enriched on active chromatin, here we identify PWWP2A and HDAC2 among the top interactors. PWWP2A and its paralog PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66α/β, and CHD3/4. PWWP2A competes with MBD3 for binding to MTA1, thus defining a new variant NuRD complex that is mutually exclusive with the MBD2/3 containing NuRD. In mESCs, PWWP2A/B is most enriched at highly transcribed genes. Loss of PWWP2A/B leads to increases in histone acetylation predominantly at highly expressed genes, accompanied by decreases in Pol II elongation. Collectively, these findings suggest a role for PWWP2A/B in regulating transcription through the fine-tuning of histone acetylation dynamics at actively transcribed genes. Transcription regulation requires recruitment of different epigenetic regulators to the chromatin. Here the authors provide evidence that an H3K36me3 reader PWWP2A forms a variant NuRD complex and plays a role in regulating transcription and histone acetylation dynamics.
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Affiliation(s)
- Tianyi Zhang
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Christopher J Millard
- Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
| | - Rebecca Konietzny
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Agilent Technologies, Hewlett-Packard-Str. 8, 76337, Waldbronn, Germany
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
| | - John W R Schwabe
- Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom.
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134
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Harkness TAA. Activating the Anaphase Promoting Complex to Enhance Genomic Stability and Prolong Lifespan. Int J Mol Sci 2018; 19:ijms19071888. [PMID: 29954095 PMCID: PMC6073722 DOI: 10.3390/ijms19071888] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 12/19/2022] Open
Abstract
In aging cells, genomic instability is now recognized as a hallmark event. Throughout life, cells encounter multiple endogenous and exogenous DNA damaging events that are mostly repaired, but inevitably DNA mutations, chromosome rearrangements, and epigenetic deregulation begins to mount. Now that people are living longer, more and more late life time is spent suffering from age-related disease, in which genomic instability plays a critical role. However, several major questions remain heavily debated, such as the following: When does aging start? How long can we live? In order to minimize the impact of genomic instability on longevity, it is important to understand when aging starts, and to ensure repair mechanisms remain optimal from the very start to the very end. In this review, the interplay between the stress and nutrient response networks, and the regulation of homeostasis and genomic stability, is discussed. Mechanisms that link these two networks are predicted to be key lifespan determinants. The Anaphase Promoting Complex (APC), a large evolutionarily conserved ubiquitin ligase, can potentially serve this need. Recent work demonstrates that the APC maintains genomic stability, mounts a stress response, and increases longevity in yeast. Furthermore, inhibition of APC activity by glucose and nutrient response factors indicates a tight link between the APC and the stress/nutrient response networks.
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Affiliation(s)
- Troy A A Harkness
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
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Lin Z, Lu Y, Meng Q, Wang C, Li X, Yang Y, Xin X, Zheng Q, Xu J, Gui X, Li T, Pu H, Xiong W, Li J, Jia S, Lu D. miR372 Promotes Progression of Liver Cancer Cells by Upregulating erbB-2 through Enhancement of YB-1. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 11:494-507. [PMID: 29858084 PMCID: PMC5992473 DOI: 10.1016/j.omtn.2018.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 03/30/2018] [Accepted: 04/04/2018] [Indexed: 12/16/2022]
Abstract
MicroRNAs are known to be involved in carcinogenesis. Recently, microRNA-372 (miR372) has been proven to play a substantial role in several human cancers, but its functions in liver cancer remain unclear. Herein, our results demonstrate that miR372 accelerates growth of liver cancer cells in vitro and in vivo. Mechanistically, miR372 enhances expression of Y-box-binding protein 1 (YB-1) by targeting for phosphatase and tensin homolog (PTEN) directly and consequently promotes phosphorylation of YB-1 via HULC looping dependent on ERK1/2 and PTEN. In particular, HULC knockdown or PTEN overexpression abrogated this miR372 action. Moreover, miR372 inhibits the degradation of β-catenin dependent on phosphorylation of YB-1 and then enhances the expression and activity of pyruvate kinase M2 isoform (PKM2) by β-catenin-LEF/TCF4 pathway. Furthermore, the loading of LEF/TCF4 on PKM2 promoter region was significantly increased in miR372 overexpressing Hep3B, and thus, glycolytic proton efflux rate (glycoPER) was significantly increased in rLV-miR372 group compared to the rLV group. Moreover, β-catenin knockdown abrogates this function of miR372. Ultimately, miR372 promotes the expression of erbB-2 through PKM2-pH3T11-acetylation on histone H3 lysine 9 (H3K9Ac) pathway. Of significance, both YB-1 knockdown and erbB-2 knockdown abrogate oncogenic action of miR372. Our observations suggest that miR372 promotes liver cancer cell cycle progress by activating cyclin-dependent kinase 2 (CDK2)-cyclin E-P21/Cip1 complex through miR372-YB-1-β-catenin-LEF/TCF4-PKM2-erbB-2 axis. This study elucidates a novel mechanism for miR372 in liver cancer cells and suggests that miR372 can be used as a novel therapeutic target of liver cancer.
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Affiliation(s)
- Zhuojia Lin
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yanan Lu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Qiuyu Meng
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Chen Wang
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Xiaonan Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yuxin Yang
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Xiaoru Xin
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Qidi Zheng
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jie Xu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Xin Gui
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Tianming Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Hu Pu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Wujun Xiong
- Department of Hepatology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jiao Li
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Song Jia
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Dongdong Lu
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
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136
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Muhammad K, Rudolf R, Pham DAT, Klein-Hessling S, Takata K, Matsushita N, Ellenrieder V, Kondo E, Serfling E. Induction of Short NFATc1/αA Isoform Interferes with Peripheral B Cell Differentiation. Front Immunol 2018; 9:32. [PMID: 29416540 PMCID: PMC5787671 DOI: 10.3389/fimmu.2018.00032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/04/2018] [Indexed: 11/15/2022] Open
Abstract
In lymphocytes, immune receptor signals induce the rapid nuclear translocation of preformed cytosolic NFAT proteins. Along with co-stimulatory signals, persistent immune receptor signals lead to high levels of NFATc1/αA, a short NFATc1 isoform, in effector lymphocytes. Whereas NFATc1 is not expressed in plasma cells, in germinal centers numerous centrocytic B cells express nuclear NFATc1/αA. When overexpressed in chicken DT40 B cells or murine WEHI 231 B cells, NFATc1/αA suppressed their cell death induced by B cell receptor signals and affected the expression of genes controlling the germinal center reaction and plasma cell formation. Among those is the Prdm1 gene encoding Blimp-1, a key factor of plasma cell formation. By binding to a regulatory DNA element within exon 1 of the Prdm1 gene, NFATc1/αA suppresses Blimp-1 expression. Since expression of a constitutive active version of NFATc1/αA interfered with Prdm1 RNA expression, LPS-mediated differentiation of splenic B cells to plasmablasts in vitro and reduced immunoglobulin production in vivo, one may conclude that NFATc1/αA plays an important role in controlling plasmablast/plasma cell formation.
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Affiliation(s)
- Khalid Muhammad
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center (CCC) Mainfranken, University of Würzburg, Würzburg, Germany
| | - Ronald Rudolf
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center (CCC) Mainfranken, University of Würzburg, Würzburg, Germany
| | - Duong Anh Thuy Pham
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center (CCC) Mainfranken, University of Würzburg, Würzburg, Germany
| | - Stefan Klein-Hessling
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center (CCC) Mainfranken, University of Würzburg, Würzburg, Germany
| | - Katsuyoshi Takata
- Department of Pathology, Graduate School of Medicine, Dentistry and Pharmaceutical Science, Okayama University, Okayama, Japan
| | - Nobuko Matsushita
- Laboratory of Molecular Biochemistry, School of Life Science, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo, Japan
| | - Volker Ellenrieder
- Department of Gastroenterology and Gastrointestinal Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Eisaku Kondo
- Division of Oncological Pathology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Edgar Serfling
- Department of Molecular Pathology, Institute of Pathology, Comprehensive Cancer Center (CCC) Mainfranken, University of Würzburg, Würzburg, Germany
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137
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Huang D, Lan W, Li D, Deng B, Lin W, Ren Y, Miao Y. WHIRLY1 Occupancy Affects Histone Lysine Modification and WRKY53 Transcription in Arabidopsis Developmental Manner. FRONTIERS IN PLANT SCIENCE 2018; 9:1503. [PMID: 30405658 PMCID: PMC6202938 DOI: 10.3389/fpls.2018.01503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 09/26/2018] [Indexed: 05/21/2023]
Abstract
Single-stranded DNA-binding proteins (SSBs) are assumed to involve in DNA replication, DNA repairmen, and gene transcription. Here, we provide the direct evidence on the functionality of an Arabidopsis SSB, WHIRLY1, by using loss- or gain-of-function lines. We show that WHIRLY1 binding to the promoter of WRKY53 represses the enrichment of H3K4me3, but enhances the enrichment of H3K9ac at the region contained WHIRLY1-binding sequences and TATA box or the translation start region of WRKY53, coincided with a recruitment of RNAPII. In vitro ChIP assays confirm that WHIRLY1 inhibits H3K4me3 enrichment at the preinitiation complex formation stage, while promotes H3K9ac enrichment and RNAPII recruitment at the elongation stage, consequently affecting the transcription of WRKY53. These results further explore the molecular actions underlying SSB-mediated gene transcription through epigenetic regulation in plant senescence.
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138
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Gates LA, Foulds CE, O'Malley BW. Histone Marks in the 'Driver's Seat': Functional Roles in Steering the Transcription Cycle. Trends Biochem Sci 2017; 42:977-989. [PMID: 29122461 DOI: 10.1016/j.tibs.2017.10.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/16/2017] [Indexed: 12/27/2022]
Abstract
Particular chromatin modifications are associated with different states of gene transcription, yet our understanding of which modifications are causal 'drivers' in promoting transcription is incomplete. Here, we discuss new developments describing the ordered, mechanistic role of select histone marks occurring during distinct steps in the RNA polymerase II (Pol II) transcription cycle. In particular, we highlight the interplay between histone marks in specifying the 'next step' of transcription. While many studies have described correlative relationships between histone marks and their occupancy at distinct gene regions, we focus on studies that elucidate clear functional consequences of specific histone marks during different stages of transcription. These recent discoveries have refined our current mechanistic understanding of how histone marks promote Pol II transcriptional progression.
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Affiliation(s)
- Leah A Gates
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Current address: Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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