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Meza-Menchaca T, Albores-Medina A, Heredia-Mendez AJ, Ruíz-May E, Ricaño-Rodríguez J, Gallegos-García V, Esquivel A, Vettoretti-Maldonado G, Campos-Parra AD. Revisiting Epigenetics Fundamentals and Its Biomedical Implications. Int J Mol Sci 2024; 25:7927. [PMID: 39063168 PMCID: PMC11276703 DOI: 10.3390/ijms25147927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
In light of the post-genomic era, epigenetics brings about an opportunity to better understand how the molecular machinery works and is led by a complex dynamic set of mechanisms, often intricate and complementary in many aspects. In particular, epigenetics links developmental biology and genetics, as well as many other areas of knowledge. The present work highlights substantial scopes and relevant discoveries related to the development of the term from its first notions. To our understanding, the concept of epigenetics needs to be revisited, as it is one of the most relevant and multifaceted terms in human knowledge. To redirect future novel experimental or theoretical efforts, it is crucial to compile all significant issues that could impact human and ecological benefit in the most precise and accurate manner. In this paper, the reader can find one of the widest compilations of the landmarks and epistemic considerations of the knowledge of epigenetics across the history of biology from the earliest epigenetic formulation to genetic determinism until the present. In the present work, we link the current body of knowledge and earlier pre-genomic concepts in order to propose a new definition of epigenetics that is faithful to its regulatory nature.
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Affiliation(s)
- Thuluz Meza-Menchaca
- Laboratorio de Investigación en Ciencias Médico-Biológicas, Facultad de Medicina, Universidad Veracruzana, Médicos y Odontólogos s/n, Col. Unidad del Bosque, Xalapa 91010, Mexico; (A.J.H.-M.); (A.E.); (G.V.-M.)
| | - Arnulfo Albores-Medina
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México 07360, Mexico;
| | - Alma Jaqueline Heredia-Mendez
- Laboratorio de Investigación en Ciencias Médico-Biológicas, Facultad de Medicina, Universidad Veracruzana, Médicos y Odontólogos s/n, Col. Unidad del Bosque, Xalapa 91010, Mexico; (A.J.H.-M.); (A.E.); (G.V.-M.)
| | - Eliel Ruíz-May
- Red de Estudios Moleculares Avanzados, Cluster BioMimic®, Instituto de Ecología A. C., Carretera Antigua a Coatepec 351, Congregación el Haya, Xalapa 91073, Mexico;
| | - Jorge Ricaño-Rodríguez
- Centro de Eco-Alfabetización y Diálogo de Saberes, Universidad Veracruzana, Zona Universitaria, Xalapa 91090, Mexico;
| | - Verónica Gallegos-García
- Facultad de Enfermería y Nutrición, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico;
| | - Adriana Esquivel
- Laboratorio de Investigación en Ciencias Médico-Biológicas, Facultad de Medicina, Universidad Veracruzana, Médicos y Odontólogos s/n, Col. Unidad del Bosque, Xalapa 91010, Mexico; (A.J.H.-M.); (A.E.); (G.V.-M.)
| | - Giancarlo Vettoretti-Maldonado
- Laboratorio de Investigación en Ciencias Médico-Biológicas, Facultad de Medicina, Universidad Veracruzana, Médicos y Odontólogos s/n, Col. Unidad del Bosque, Xalapa 91010, Mexico; (A.J.H.-M.); (A.E.); (G.V.-M.)
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Suvekbala V, Ramachandran H, Veluchamy A, Mascarenhas MAB, Ramprasath T, Nair MKC, Garikipati VNS, Gundamaraju R, Subbiah R. The Promising Epigenetic Regulators for Refractory Epilepsy: An Adventurous Road Ahead. Neuromolecular Med 2022:10.1007/s12017-022-08723-0. [DOI: 10.1007/s12017-022-08723-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/13/2022] [Indexed: 10/14/2022]
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Song A, Chen FX. The pleiotropic roles of SPT5 in transcription. Transcription 2022; 13:53-69. [PMID: 35876486 PMCID: PMC9467590 DOI: 10.1080/21541264.2022.2103366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Initially discovered by genetic screens in budding yeast, SPT5 and its partner SPT4 form a stable complex known as DSIF in metazoa, which plays pleiotropic roles in multiple steps of transcription. SPT5 is the most conserved transcription elongation factor, being found in all three domains of life; however, its structure has evolved to include new domains and associated posttranslational modifications. These gained features have expanded transcriptional functions of SPT5, likely to meet the demand for increasingly complex regulation of transcription in higher organisms. This review discusses the pleiotropic roles of SPT5 in transcription, including RNA polymerase II (Pol II) stabilization, enhancer activation, Pol II pausing and its release, elongation, and termination, with a focus on the most recent progress of SPT5 functions in regulating metazoan transcription.
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Affiliation(s)
- Aixia Song
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, Province 200032, China
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, Province 200032, China
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Viral Manipulation of the Host Epigenome as a Driver of Virus-Induced Oncogenesis. Microorganisms 2021; 9:microorganisms9061179. [PMID: 34070716 PMCID: PMC8227491 DOI: 10.3390/microorganisms9061179] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022] Open
Abstract
Tumorigenesis due to viral infection accounts for a high fraction of the total global cancer burden (15–20%) of all human cancers. A comprehensive understanding of the mechanisms by which viral infection leads to tumor development is extremely important. One of the main mechanisms by which viruses induce host cell proliferation programs is through controlling the host’s epigenetic machinery. In this review, we dissect the epigenetic pathways through which oncogenic viruses can integrate their genome into host cell chromosomes and lead to tumor progression. In addition, we highlight the potential use of drugs based on histone modifiers in reducing the global impact of cancer development due to viral infection.
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Noncoding RNAs Set the Stage for RNA Polymerase II Transcription. Trends Genet 2020; 37:279-291. [PMID: 33046273 DOI: 10.1016/j.tig.2020.09.013] [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: 07/18/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/24/2022]
Abstract
Effective synthesis of mammalian messenger (m)RNAs depends on many factors that together direct RNA polymerase II (pol II) through the different stages of the transcription cycle and ensure efficient cotranscriptional processing of mRNAs. In addition to the many proteins involved in transcription initiation, elongation, and termination, several noncoding (nc)RNAs also function as global transcriptional regulators. Understanding the mode of action of these non-protein regulators has been an intense area of research in recent years. Here, we describe how these ncRNAs influence key regulatory steps of the transcription process, to affect large numbers of genes. Through direct association with pol II or by modulating the activity of transcription or RNA processing factors, these regulatory RNAs perform critical roles in gene expression.
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Non-Coding RNA Editing in Cancer Pathogenesis. Cancers (Basel) 2020; 12:cancers12071845. [PMID: 32650588 PMCID: PMC7408896 DOI: 10.3390/cancers12071845] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
In the last two decades, RNA post-transcriptional modifications, including RNA editing, have been the subject of increasing interest among the scientific community. The efforts of the Human Genome Project combined with the development of new sequencing technologies and dedicated bioinformatic approaches created to detect and profile RNA transcripts have served to further our understanding of RNA editing. Investigators have determined that non-coding RNA (ncRNA) A-to-I editing is often deregulated in cancer. This discovery has led to an increased number of published studies in the field. However, the eventual clinical application for these findings remains a work in progress. In this review, we provide an overview of the ncRNA editing phenomenon in cancer. We discuss the bioinformatic strategies for RNA editing detection as well as the potential roles for ncRNA A to I editing in tumor immunity and as clinical biomarkers.
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Mohanta TK, Yadav D, Khan A, Hashem A, Tabassum B, Khan AL, Abd_Allah EF, Al-Harrasi A. Genomics, molecular and evolutionary perspective of NAC transcription factors. PLoS One 2020; 15:e0231425. [PMID: 32275733 PMCID: PMC7147800 DOI: 10.1371/journal.pone.0231425] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/23/2020] [Indexed: 01/05/2023] Open
Abstract
NAC (NAM, ATAF1,2, and CUC2) transcription factors are one of the largest transcription factor families found in the plants and are involved in diverse developmental and signalling events. Despite the availability of comprehensive genomic information from diverse plant species, the basic genomic, biochemical, and evolutionary details of NAC TFs have not been established. Therefore, NAC TFs family proteins from 160 plant species were analyzed in the current study. Study revealed, Brassica napus (410) encodes highest number and Klebsormidium flaccidum (3) encodes the lowest number of TFs. The study further revealed the presence of NAC TF in the Charophyte algae K. flaccidum. On average, the monocot plants encode higher number (141.20) of NAC TFs compared to the eudicots (125.04), gymnosperm (75), and bryophytes (22.66). Furthermore, our analysis revealed that several NAC TFs are membrane bound and contain monopartite, bipartite, and multipartite nuclear localization signals. NAC TFs were also found to encode several novel chimeric proteins and regulate a complex interactome network. In addition to the presence of NAC domain, several NAC proteins were found to encode other functional signature motifs as well. Relative expression analysis of NAC TFs in A. thaliana revealed root tissue treated with urea and ammonia showed higher level of expression and leaf tissues treated with urea showed lower level of expression. The synonymous codon usage is absent in the NAC TFs and it appears that they have evolved from orthologous ancestors and undergone vivid duplications to give rise to paralogous NAC TFs. The presence of novel chimeric NAC TFs are of particular interest and the presence of chimeric NAC domain with other functional signature motifs in the NAC TF might encode novel functional properties in the plants.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Dhananjay Yadav
- Dept. of Medical Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Adil Khan
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, Egypt
| | - Baby Tabassum
- Department of Zoology, Toxicology laboratory, Raza P.G. College, Rampur, Uttar Pradesh, India
| | - Abdul Latif Khan
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Al-Harrasi
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
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Espinosa JM. Transcriptional control by enhancers: working remotely for improved performance. Transcription 2020; 11:1-2. [PMID: 32054432 DOI: 10.1080/21541264.2020.1724673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Joaquin M Espinosa
- Linda Crnic Institute for Down Syndrome & Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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