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Moelling K. Epigenetics and transgenerational inheritance. J Physiol 2024; 602:2537-2545. [PMID: 37772441 DOI: 10.1113/jp284424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Epigenetic modifications can alter the function of genes. The epigenetics changes are caused by environmental effects, which lead to chemical modifications of the DNA or the chromatin. The mechanisms involve the influence of small interfering siRNAs on gene silencing. Epigenetic changes normally last only during the life-time of an individual and are erased in embryos and eggs for a naive progeny. The genomes are reprogrammed and the chemical modifications removed to restart the next generation. However, there are mechanisms that allow the genome to escape from such a clearing effect so that modifications can be transmitted to one or more subsequent generations. In the germline of animal cells small RNAs, including piRNAs, have evolved which guarantee a higher degree of fidelity for transmission of genetic information, guarding especially against the detrimental effect caused by transposon activity. piRNA is essential for transposon silencing for survival of a species and protection of subsequent generations. Inactivation of piRNA results in abundant transposon activity and sperm infertility. The effect in humans has been described but is less distinct. Some stress-induced epigenetic changes are transitory in mice and can be reversed by a change of environment or lifestyle.
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Affiliation(s)
- Karin Moelling
- Institute Medical Microbiology, University Zürich, Zurich, Switzerland
- Max Planck Institute of Molecular Genetics, Berlin, Germany
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Mukhopadhyay P, Miller H, Stoja A, Bishop AJR. Approaches for Mapping and Analysis of R-loops. Curr Protoc 2024; 4:e1037. [PMID: 38666626 DOI: 10.1002/cpz1.1037] [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: 05/04/2024]
Abstract
R-loops are nucleic acid structures composed of a DNA:RNA hybrid with a displaced non-template single-stranded DNA. Current approaches to identify and map R-loop formation across the genome employ either an antibody targeted against R-loops (S9.6) or a catalytically inactivated form of RNase H1 (dRNH1), a nuclease that can bind and resolve DNA:RNA hybrids via RNA exonuclease activity. This overview article outlines several ways to map R-loops using either methodology, explaining the differences and similarities among the approaches. Bioinformatic analysis of R-loops involves several layers of quality control and processing before visualizing the data. This article provides resources and tools that can be used to accurately process R-loop mapping data and explains the advantages and disadvantages of the resources as compared to one another. © 2024 Wiley Periodicals LLC.
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Affiliation(s)
- Pramiti Mukhopadhyay
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | | | - Aiola Stoja
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | - Alexander J R Bishop
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
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Kocyigit I, Taheri S, Uysal C, Memis M, Ozayturk SG, Zararsiz G, Rassoulzadegan M. Predicting Progression of Autosomal Dominant Polycystic Kidney Disease by Changes in the Telomeric Epigenome. Cells 2022; 11:cells11203300. [PMID: 36291168 PMCID: PMC9600909 DOI: 10.3390/cells11203300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited cause of chronic kidney disease with Polycystin (PKD) 1 and 2 gene mutation. However, the intra-familial variability in symptoms further suggests a non-Mendelian contribution to the disease. Our goal was to find a marker to track the epigenetic changes common to rapidly progressing forms of the disease. The risk of ADPKD increases with age, and aging shortens the telomere length (TL). Telomeres are a nucleoprotein structure composed mainly of three complexes, shelterin, CST and RNA-containing telomere repeat(TERRA), which protects the ends of chromosomes from degradation and fusion, and plays a role in maintaining cellular stability and in the repair of telomeric damage. TERRAs are transcribed from telomeric regions and a part of them is engaged in a DNA/RNA hybrid (R-loop) at each chromosome end. We tracked TL and TERRA levels in blood samples of 78 patients and 20 healthy control. Our study demonstrates that TL was shortened and TERRA expression levels in the DNA-attached fraction increased in autosomal dominant polycystic kidney patients with mutations in PKD1 and PKD2 compared to the control group. Moreover, it was observed that the expression of TERRA engaged in the R-loop was higher and the length of telomeres shorter in patients with ADPKD who showed rapid disease progression. Intrafamilial variation in TL and TERRA levels with the same mutation would indicate reliable epigenetic potential biomarkers in disease monitoring.
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Affiliation(s)
- Ismail Kocyigit
- Department of Nephrology, Medical School, Erciyes University, 38280 Kayseri, Turkey
- Correspondence:
| | - Serpil Taheri
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey
- Department of Medical Biology, Medical School, Erciyes University, 38280 Kayseri, Turkey
| | - Cihan Uysal
- Department of Nephrology, Medical School, Erciyes University, 38280 Kayseri, Turkey
| | - Mehmet Memis
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey
| | - Salih Guntug Ozayturk
- Department of Internal Medicine, Medical School, Erciyes University, 38280 Kayseri, Turkey
| | - Gokmen Zararsiz
- Department of Biostatistics, Medical School, Erciyes University, 38280 Kayseri, Turkey
| | - Minoo Rassoulzadegan
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey
- INSERM-CNRS, Université de Nice, 06107 Nice, France
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Satir-Basaran G, Kianmehr L, Mehmetbeyoglu E, Korkmaz Bayram K, Memis M, Yilmaz Z, Tufan E, Taheri S, Kelestimur F, Rassoulzadegan M. Mouse Paternal RNAs Initiate a Pattern of Metabolic Disorders in a Line-Dependent Manner. Front Genet 2022; 13:839841. [PMID: 35419033 PMCID: PMC8996111 DOI: 10.3389/fgene.2022.839841] [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] [Received: 12/20/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
A wide range of diseases result from environmental effects, and the levels of many native transcripts are altered. The alteration of non-coding RNAs (ncRNAs) and transmission of the variation to the next generation is increasingly recognized as a marker of disease. However, the determining signals and mechanisms of RNA-induced heritability remain unclear. We performed functional tests with four different genotypes of mice maintained on a high-fat diet to trace the transfer of the obesity/diabetes phenotype to the next generation in order to detect common signals. Two founders of four mouse lines (B6/D2 hybrid and Dnmt2 -/-C57BL/6 ) resist and do not change their phenotype while their sperm RNAs after microinjection into fertilized mouse eggs transfer the newly acquired phenotypes in a susceptible inbred line (C57BL/6 or Balb/c). Unexpectedly, in the same line of experiments, sperm RNA from animals raised on a normal diet when mixed with the sperm RNA from animals raised on a diet high in fat or synthetic miR-19b (inducer of obesity) affects or prevents the development of obesity and diabetes. However, it remains unclear what happens to ncRNA signaling under diet. With a comprehensive new analysis of the transcripts maintained as an RNA/DNA hybrid in sperm, we suggest that a fraction of the RNAs are stably attached to the genome. Thus, we propose that changes in the dynamics of ncRNA retention on DNA by factors such as transcriptional variations or lack of adequate methylation could serve as molecular markers to trace these epigenetics events.
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Affiliation(s)
- Guzide Satir-Basaran
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey.,Department of Biochemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Leila Kianmehr
- Departement of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Ecmel Mehmetbeyoglu
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey.,Department of Cancer and Genetics, Cardiff University, Cardiff, United Kingdom
| | - Kezban Korkmaz Bayram
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey.,Department of Medical Genetics, Medical Faculty, Yıldırım Beyazıt University, 06800 Ankara, Turkey
| | - Mehmet Memis
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey
| | - Zeynep Yilmaz
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey
| | - Esra Tufan
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey
| | - Serpil Taheri
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey.,Department of Medical Biology, Erciyes University Medical School, Kayseri, Turkey
| | - Fahrettin Kelestimur
- Department of Endocrinology, Yeditepe University Medical School, Istanbul, Turkey
| | - Minoo Rassoulzadegan
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey.,INSERM-CNRS, Université de Nice, Nice, France
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Mehmetbeyoglu E, Kianmehr L, Borlu M, Yilmaz Z, Basar Kılıc S, Rajabi-Maham H, Taheri S, Rassoulzadegan M. Decrease in RNase HII and Accumulation of lncRNAs/DNA Hybrids: A Causal Implication in Psoriasis? Biomolecules 2022; 12:biom12030368. [PMID: 35327560 PMCID: PMC8945458 DOI: 10.3390/biom12030368] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
Abstract
Functional long non-coding RNAs (lncRNAs) have been in the limelight in aging research because short telomeres are associated with higher levels of TERRA (Telomeric Repeat containing RNA). The genomic instability, which leads to short telomeres, is a mechanism observed in cell aging and in a class of cancer cells. Psoriasis, a skin disease, is a disorder of epidermal keratinocytes, with altered telomerase activity. Research on the fraction of nascent RNAs in hybrid with DNA offers avenues for new strategies. Skin and blood samples from patients were fractionated to obtain the RNA associated with DNA as a R-loop structure. The higher amount of TERRA levels attached with each chromosome end was found with psoriasis patients in blood and skin. In addition to telomeric TERRA, we evidenced accumulation of others non-coding RNA, such as non-telomeric TERRA and centromeric transcripts. Increased levels of non-coding RNAs attached to DNA correlates with a decreased in Ribonuclease HII (RNase-HII) transcript which means that overall unresolved DNA–RNA hybrids can ultimately weaken DNA and cause skin lesions. Since the genome is actively transcribed, cellular RNase-HII is essential for removing RNA from the DNA–RNA hybrid in controls of genome stability and epigenome shaping and can be used as a causal prognostic marker in patients with psoriasis.
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Affiliation(s)
- Ecmel Mehmetbeyoglu
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey; (E.M.); (Z.Y.)
- Department of Medical Biology, Medical Faculty, Erciyes University, 38280 Kayseri, Turkey
| | - Leila Kianmehr
- Animal Sciences and Marine Biology Department, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 1983963411, Iran; (H.R.-M.); (L.K.)
| | - Murat Borlu
- Dermatology and Venereology Department, Medical School, Erciyes University, 38280 Kayseri, Turkey;
| | - Zeynep Yilmaz
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey; (E.M.); (Z.Y.)
- Department of Medical Biology, Medical Faculty, Erciyes University, 38280 Kayseri, Turkey
| | - Seyma Basar Kılıc
- Dermatology and Venereology Department, Training and Research Hospital, Aksaray University, 68000 Aksaray, Turkey;
| | - Hassan Rajabi-Maham
- Animal Sciences and Marine Biology Department, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran 1983963411, Iran; (H.R.-M.); (L.K.)
| | - Serpil Taheri
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey; (E.M.); (Z.Y.)
- Department of Medical Biology, Medical Faculty, Erciyes University, 38280 Kayseri, Turkey
- Correspondence: (S.T.); (M.R.)
| | - Minoo Rassoulzadegan
- Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, 38280 Kayseri, Turkey; (E.M.); (Z.Y.)
- INSERM-CNRS, Université de Nice, 06000 Nice, France
- Correspondence: (S.T.); (M.R.)
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Genome-wide investigations on regulatory functions of RECQ1 helicase. Methods 2022; 204:263-268. [PMID: 35231585 PMCID: PMC9233132 DOI: 10.1016/j.ymeth.2022.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 01/10/2023] Open
Abstract
DNA helicase RECQ1 (also known as RECQL or RECQL1) is a candidate breast cancer susceptibility gene significantly correlated with clinical outcomes of sporadic breast cancer patients. Prior studies have suggested that RECQ1 maintains genomic stability by regulating a wide variety of core cellular functions including DNA replication, DNA damage response, and transcription. However, it is unclear which, if any, of these are the primary functions of RECQ1 as related to its role in suppressing breast cancer. We describe here an unbiased integrative genomics approach that enabled us to discover a previously unknown regulatory role of RECQ1 in promoting Estrogen Receptor alpha (ERα) expression and the expression of specific ERα target genes in ER positive breast cancer cells. We discuss potential future applications of similar experimental strategies in advancing the mechanistic understanding and elucidating specific new details of genome-wide functions of RECQ1 and other RecQ helicases in maintaining genomic stability and preventing cancer.
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