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Arunkumar G. LncRNAs: the good, the bad, and the unknown. Biochem Cell Biol 2024; 102:9-27. [PMID: 37579511 DOI: 10.1139/bcb-2023-0155] [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] [Indexed: 08/16/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are significant contributors in maintaining genomic integrity through epigenetic regulation. LncRNAs can interact with chromatin-modifying complexes in both cis and trans pathways, drawing them to specific genomic loci and influencing gene expression via DNA methylation, histone modifications, and chromatin remodeling. They can also operate as building blocks to assemble different chromatin-modifying components, facilitating their interactions and gene regulatory functions. Deregulation of these molecules has been associated with various human diseases, including cancer, cardiovascular disease, and neurological disorders. Thus, lncRNAs are implicated as potential diagnostic indicators and therapeutic targets. This review discusses the current understanding of how lncRNAs mediate epigenetic control, genomic integrity, and their putative functions in disease pathogenesis.
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Affiliation(s)
- Ganesan Arunkumar
- The LncRNA, Epigenetics, and Genome Organization Laboratory, Department of Cell Biology and Physiology, School of Medicine, University of New Mexico, Albuquerque, NM, USA
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de Almeida BRR, Farias Souza L, Alves TA, Cardoso AL, de Oliveira JA, Augusto Ribas TF, Dos Santos CEV, do Nascimento LAS, Sousa LM, da Cunha Sampaio MI, Martins C, Nagamachi CY, Pieczarka JC, Noronha RCR. Chromosomal organization of multigene families and meiotic analysis in species of Loricariidae (Siluriformes) from Brazilian Amazon, with description of a new cytotype for genus Spatuloricaria. Biol Open 2023; 12:bio060029. [PMID: 37819723 PMCID: PMC10651099 DOI: 10.1242/bio.060029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
In the Amazon, some species of Loricariidae are at risk of extinction due to habitat loss and overexploitation by the ornamental fish market. Cytogenetic data related to the karyotype and meiotic cycle can contribute to understanding the reproductive biology and help management and conservation programs of these fish. Additionally, chromosomal mapping of repetitive DNA in Loricariidae may aid comparative genomic studies in this family. However, cytogenetics analysis is limited in Amazonian locariids. In this study, chromosomal mapping of multigenic families was performed in Scobinancistrus aureatus, Scobinancistrus pariolispos and Spatuloricaria sp. Meiotic analyzes were performed in Hypancistrus zebra and Hypancistrus sp. "pão". Results showed new karyotype for Spatuloricaria sp. (2n=66, NF=82, 50m-10sm-6m). Distinct patterns of chromosomal organization of histone H1, histone H3 and snDNA U2 genes were registered in the karyotypes of the studied species, proving to be an excellent cytotaxonomic tool. Hypotheses to explain the evolutionary dynamics of these sequences in studied Loricariidae were proposed. Regarding H. zebra and H. sp. "pão", we describe the events related to synapse and transcriptional activity during the meiotic cycle, which in both species showed 26 fully synapsed bivalents, with high gene expression only during zygotene and pachytene. Both Hypancistrus species could be used may be models for evaluating changes in spermatogenesis of Loricariidae.
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Affiliation(s)
- Bruno Rafael Ribeiro de Almeida
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Pará. Campus Itaituba. Itaituba, 68183-300, Pará, Brazil
| | - Luciano Farias Souza
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Thyana Ayres Alves
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Adauto Lima Cardoso
- Laboratório Genômica Integrativa, Instituto de Biociências, Universidade Estadual Paulista. Botucatu, CEP 18618-970, São Paulo, Brazil
| | - Juliana Amorim de Oliveira
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Talita Fernanda Augusto Ribas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Carlos Eduardo Vasconcelos Dos Santos
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | | | - Leandro Melo Sousa
- Faculdade de Ciências Biológicas, Universidade Federal do Pará, Campus de Altamira. Altamira, CEP 68372-040, Pará, Brazil
| | - Maria Iracilda da Cunha Sampaio
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Universitário de Bragança.. Bragança, CEP 68600-000, Pará, Brazil
| | - Cesar Martins
- Laboratório Genômica Integrativa, Instituto de Biociências, Universidade Estadual Paulista. Botucatu, CEP 18618-970, São Paulo, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Genética e Biologia Celular, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará. Belém 66075-750, Pará, Brazil
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Santini GT, Shah PP, Karnay A, Jain R. Aberrant chromatin organization at the nexus of laminopathy disease pathways. Nucleus 2022; 13:300-312. [PMID: 36503349 PMCID: PMC9746625 DOI: 10.1080/19491034.2022.2153564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Garrett T. Santini
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Parisha P. Shah
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Ashley Karnay
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Rajan Jain
- Departments of Medicine and Cell and Developmental Biology, Penn Cardiovascular Institute, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA,CONTACT Rajan Jain Smilow Center for Translational Research, 09-101 3400 Civic Center Blvd, PhiladelphiaPA 19104
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Mustafin RN, Khusnutdinova EK. The relationship of lamins with epigenetic factors during aging. Vavilovskii Zhurnal Genet Selektsii 2022; 26:40-49. [PMID: 35342861 PMCID: PMC8892175 DOI: 10.18699/vjgb-22-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/23/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022] Open
Abstract
The key factor of genome instability during aging is transposon dysregulation. This may be due to senile changes in the expression of lamins, which epigenetically modulate transposons. Lamins directly physically interact with transposons. Epigenetic regulators such as SIRT7, BAF, and microRNA can also serve as intermediaries for their interactions. There is also an inverse regulation, since transposons are sources of miRNAs that affect lamins. We suggest that lamins can be attributed to epigenetic factors, since they are part of the NURD, interact with histone deacetylases and regulate gene expression without changing the nucleotide sequences. The role of lamins in the etiopathogenesis of premature aging syndromes may be associated with interactions with transposons. In various human cells, LINE1 is present in the heterochromatin domains of the genome associated with lamins, while SIRT7 facilitates the interaction of this retroelement with lamins. Both retroelements and the nuclear lamina play an important role in the antiviral response of organisms. This may be due to the role of lamins in protection from both viruses and transposons, since viruses and transposons are evolutionarily related. Transposable elements and lamins are secondary messengers of environmental stressors that can serve as triggers for aging and carcinogenesis. Transposons play a role in the development of cancer, while the microRNAs derived from them, participating in the etiopathogenesis of tumors, are important in human aging. Lamins have similar properties, since lamins are dysregulated in cancer, and microRNAs affecting them are involved in carcinogenesis. Changes in the expression of specif ic microRNAs were also revealed
in laminopathies. Identif ication of the epigenetic mechanisms of interaction of lamins with transposons during
aging
can become the basis for the development of methods of life extension and targeted therapy of age-associated
cancer
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Affiliation(s)
| | - E. K. Khusnutdinova
- Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences
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Retrotransposons Down- and Up-Regulation in Aging Somatic Tissues. Cells 2021; 11:cells11010079. [PMID: 35011640 PMCID: PMC8750722 DOI: 10.3390/cells11010079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 01/19/2023] Open
Abstract
The transposon theory of aging hypothesizes the activation of transposable elements (TEs) in somatic tissues with age, leading to a shortening of the lifespan. It is thought that TE activation in aging produces an increase in DNA double-strand breaks, contributing to genome instability and promoting the activation of inflammatory responses. To investigate how TE regulation changes in somatic tissues during aging, we analyzed the expression of some TEs, as well as a source of small RNAs that specifically silence the analyzed TEs; the Drosophila cluster named flamenco. We found significant variations in the expression levels of all the analyzed TEs during aging, with a trend toward reduction in middle-aged adults and reactivation in older individuals that suggests dynamic regulation during the lifespan.
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The Impact of Drosophila Awd/NME1/2 Levels on Notch and Wg Signaling Pathways. Int J Mol Sci 2020; 21:ijms21197257. [PMID: 33019537 PMCID: PMC7582475 DOI: 10.3390/ijms21197257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/18/2020] [Accepted: 09/29/2020] [Indexed: 01/09/2023] Open
Abstract
Awd, the Drosophila homologue of NME1/2 metastasis suppressors, plays key roles in many signaling pathways. Mosaic analysis of the null awdJ2A4 allele showed that loss of awd gene function blocks Notch signaling and the expression of its target genes including the Wingless (Wg/Wnt1) morphogen. We also showed that RNA interference (RNAi)-mediated awd silencing (awdi) in larval wing disc leads to chromosomal instability (CIN) and to Jun amino-terminal kinases (JNK)-mediated cell death. Here we show that this cell death is independent of p53 activity. Based on our previous finding showing that forced survival of awdi-CIN cells leads to aneuploidy without the hyperproliferative effect, we investigated the Wg expression in awdi wing disc cells. Interestingly, the Wg protein is expressed in its correct dorso-ventral domain but shows an altered cellular distribution which impairs its signaling. Further, we show that RNAi-mediated knock down of awd in wing discs does not affect Notch signaling. Thus, our analysis of the hypomorphic phenotype arising from awd downregulation uncovers a dose-dependent effect of Awd in Notch and Wg signaling.
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