1
|
Diaz Escarcega R, Marshall P, Tsvetkov AS. G-quadruplex DNA and RNA in cellular senescence. FRONTIERS IN AGING 2024; 5:1491389. [PMID: 39444378 PMCID: PMC11496277 DOI: 10.3389/fragi.2024.1491389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Accepted: 09/25/2024] [Indexed: 10/25/2024]
Abstract
Normal cells divide, are damaged, and are repaired across their lifetime. As cells age, they enter cellular senescence, characterized by a permanent state of cell-cycle arrest triggered by various stressors. The molecular mechanisms that regulate senescent phenotypes have been actively investigated over the last several decades; however, one area that has been neglected is how G-quadruplex (G4) DNA and RNA (G4-DNA and G4-RNA) mediate senescence. These non-canonical four-stranded DNA and RNA structures regulate most normative DNA and RNA-dependent processes, such as transcription, replication, and translation, as well as pathogenic mechanisms, including genomic instability and abnormal stress granule function. This review also highlights the contribution of G4s to sex differences in age-associated diseases and emphasizes potential translational approaches to target senescence and anti-aging mechanisms through G4 manipulation.
Collapse
Affiliation(s)
- Rocio Diaz Escarcega
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX, United States
| | - Paul Marshall
- College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
| | - Andrey S. Tsvetkov
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
| |
Collapse
|
2
|
Miglierina E, Ordanoska D, Le Noir S, Laffleur B. RNA processing mechanisms contribute to genome organization and stability in B cells. Oncogene 2024; 43:615-623. [PMID: 38287115 PMCID: PMC10890934 DOI: 10.1038/s41388-024-02952-2] [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: 08/29/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
RNA processing includes post-transcriptional mechanisms controlling RNA quality and quantity to ensure cellular homeostasis. Noncoding (nc) RNAs that are regulated by these dynamic processes may themselves fulfill effector and/or regulatory functions, and recent studies demonstrated the critical role of RNAs in organizing both chromatin and genome architectures. Furthermore, RNAs can threaten genome integrity when accumulating as DNA:RNA hybrids, but could also facilitate DNA repair depending on the molecular context. Therefore, by qualitatively and quantitatively fine-tuning RNAs, RNA processing contributes directly or indirectly to chromatin states, genome organization, and genome stability. B lymphocytes represent a unique model to study these interconnected mechanisms as they express ncRNAs transcribed from key specific sequences before undergoing physiological genetic remodeling processes, including V(D)J recombination, somatic hypermutation, and class switch recombination. RNA processing actors ensure the regulation and degradation of these ncRNAs for efficient DNA repair and immunoglobulin gene remodeling while failure leads to B cell development alterations, aberrant DNA repair, and pathological translocations. This review highlights how RNA processing mechanisms contribute to genome architecture and stability, with emphasis on their critical roles during B cell development, enabling physiological DNA remodeling while preventing lymphomagenesis.
Collapse
Affiliation(s)
- Emma Miglierina
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Delfina Ordanoska
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Sandrine Le Noir
- UMR CNRS 7276, Inserm 1262, Université de Limoges: Contrôle de la Réponse Immune B et des Lymphoproliférations, Team 2, B-NATION: B cell Nuclear Architecture, Immunoglobulin genes and Oncogenes, Limoges, France
| | - Brice Laffleur
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France.
| |
Collapse
|
3
|
Ketkar A, Sewilam RS, McCrury MJ, Hall JS, Bell A, Paxton BC, Tripathi S, Gunderson JEC, Eoff RL. Conservation of the insert-2 motif confers Rev1 from different species with an ability to disrupt G-quadruplexes and stimulate translesion DNA synthesis. RSC Chem Biol 2023; 4:466-485. [PMID: 37415867 PMCID: PMC10320842 DOI: 10.1039/d3cb00027c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/08/2023] [Indexed: 07/08/2023] Open
Abstract
In some organisms, the replication of G-quadruplex (G4) structures is supported by the Rev1 DNA polymerase. We previously showed that residues in the insert-2 motif of human Rev1 (hRev1) increased the affinity of the enzyme for G4 DNA and mediated suppression of mutagenic replication near G4 motifs. We have now investigated the conservation of G4-selective properties in Rev1 from other species. We compared Rev1 from Danio rerio (zRev1), Saccharomyces cerevisiae (yRev1), and Leishmania donovani (lRev1) with hRev1, including an insert-2 mutant form of hRev1 (E466A/Y470A or EY). We found that zRev1 retained all of the G4-selective prowess of the human enzyme, but there was a marked attenuation of G4 binding affinity for the EY hRev1 mutant and the two Rev1 proteins lacking insert-2 (yRev1 and lRev1). Perhaps most strikingly, we found that insert-2 was important for disruption of the G4 structure and optimal stimulation of processive DNA synthesis across the guanine-rich motif by DNA polymerase kappa (pol κ). Our findings have implications for how Rev1 might contribute to G4 replication in different species spanning the evolutionary tree - signaling the importance of selection for enzymes with robust G4-selective properties in organisms where these non-B DNA structures may fulfill taxa-specific physiological functions.
Collapse
Affiliation(s)
- Amit Ketkar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock AR 72205 USA +1 501 686 8169 +1 501 686 8343
| | - Reham S Sewilam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock AR 72205 USA +1 501 686 8169 +1 501 686 8343
| | - Mason J McCrury
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock AR 72205 USA +1 501 686 8169 +1 501 686 8343
| | - Jaycelyn S Hall
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock AR 72205 USA +1 501 686 8169 +1 501 686 8343
| | - Ashtyn Bell
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock AR 72205 USA +1 501 686 8169 +1 501 686 8343
| | - Bethany C Paxton
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock AR 72205 USA +1 501 686 8169 +1 501 686 8343
| | - Shreyam Tripathi
- Arkansas School for Mathematics, Sciences, and the Arts Hot Springs AR 71901 USA
| | | | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock AR 72205 USA +1 501 686 8169 +1 501 686 8343
| |
Collapse
|
4
|
Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
Collapse
Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
| |
Collapse
|
5
|
Roles of G4-DNA and G4-RNA in Class Switch Recombination and Additional Regulations in B-Lymphocytes. Molecules 2023; 28:molecules28031159. [PMID: 36770824 PMCID: PMC9921937 DOI: 10.3390/molecules28031159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Mature B cells notably diversify immunoglobulin (Ig) production through class switch recombination (CSR), allowing the junction of distant "switch" (S) regions. CSR is initiated by activation-induced deaminase (AID), which targets cytosines adequately exposed within single-stranded DNA of transcribed targeted S regions, with a specific affinity for WRCY motifs. In mammals, G-rich sequences are additionally present in S regions, forming canonical G-quadruplexes (G4s) DNA structures, which favor CSR. Small molecules interacting with G4-DNA (G4 ligands), proved able to regulate CSR in B lymphocytes, either positively (such as for nucleoside diphosphate kinase isoforms) or negatively (such as for RHPS4). G4-DNA is also implicated in the control of transcription, and due to their impact on both CSR and transcriptional regulation, G4-rich sequences likely play a role in the natural history of B cell malignancies. Since G4-DNA stands at multiple locations in the genome, notably within oncogene promoters, it remains to be clarified how it can more specifically promote legitimate CSR in physiology, rather than pathogenic translocation. The specific regulatory role of G4 structures in transcribed DNA and/or in corresponding transcripts and recombination hereby appears as a major issue for understanding immune responses and lymphomagenesis.
Collapse
|
6
|
Malone EG, Thompson MD, Byrd AK. Role and Regulation of Pif1 Family Helicases at the Replication Fork. Int J Mol Sci 2022; 23:ijms23073736. [PMID: 35409096 PMCID: PMC8998199 DOI: 10.3390/ijms23073736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Pif1 helicases are a multifunctional family of DNA helicases that are important for many aspects of genomic stability in the nucleus and mitochondria. Pif1 helicases are conserved from bacteria to humans. Pif1 helicases play multiple roles at the replication fork, including promoting replication through many barriers such as G-quadruplex DNA, the rDNA replication fork barrier, tRNA genes, and R-loops. Pif1 helicases also regulate telomerase and promote replication termination, Okazaki fragment maturation, and break-induced replication. This review highlights many of the roles and regulations of Pif1 at the replication fork that promote cellular health and viability.
Collapse
Affiliation(s)
- Emory G. Malone
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
| | - Matthew D. Thompson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
| | - Alicia K. Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (E.G.M.); (M.D.T.)
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: ; Tel.: +1-501-526-6488
| |
Collapse
|
7
|
Tang C, Krantsevich A, MacCarthy T. Deep learning model of somatic hypermutation reveals importance of sequence context beyond hotspot targeting. iScience 2022; 25:103668. [PMID: 35036866 PMCID: PMC8749460 DOI: 10.1016/j.isci.2021.103668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/08/2021] [Accepted: 12/16/2021] [Indexed: 11/23/2022] Open
Abstract
B cells undergo somatic hypermutation (SHM) of the Immunoglobulin (Ig) variable region to generate high-affinity antibodies. SHM relies on the activity of activation-induced deaminase (AID), which mutates C>U preferentially targeting WRC (W=A/T, R=A/G) hotspots. Downstream mutations at WA Polymerase η hotspots contribute further mutations. Computational models of SHM can describe the probability of mutations essential for vaccine responses. Previous studies using short subsequences (k-mers) failed to explain divergent mutability for the same k-mer. We developed the DeepSHM (Deep learning on SHM) model using k-mers of size 5-21, improving accuracy over previous models. Interpretation of DeepSHM identified an extended WWRCT motif with particularly high mutability. Increased mutability was further associated with lower surrounding G content. Our model also discovered a conserved AGYCTGGGGG (Y=C/T) motif within FW1 of IGHV3 family genes with unusually high T>G substitution rates. Thus, a wider sequence context increases predictive power and identifies features that drive mutational targeting.
Collapse
Affiliation(s)
- Catherine Tang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Artem Krantsevich
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|