1
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Mondragón-Rosas F, Florencio-Martínez LE, Villa-Delavequia GS, Manning-Cela RG, Carrero JC, Nepomuceno-Mejía T, Martínez-Calvillo S. Characterization of Tau95 led to the identification of a four-subunit TFIIIC complex in trypanosomatid parasites. Appl Microbiol Biotechnol 2024; 108:109. [PMID: 38204130 PMCID: PMC10781861 DOI: 10.1007/s00253-023-12903-8] [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: 07/05/2023] [Revised: 09/20/2023] [Accepted: 09/30/2023] [Indexed: 01/12/2024]
Abstract
RNA polymerase III (RNAP III) synthetizes small essential non-coding RNA molecules such as tRNAs and 5S rRNA. In yeast and vertebrates, RNAP III needs general transcription factors TFIIIA, TFIIIB, and TFIIIC to initiate transcription. TFIIIC, composed of six subunits, binds to internal promoter elements in RNAP III-dependent genes. Limited information is available about RNAP III transcription in the trypanosomatid protozoa Trypanosoma brucei and Leishmania major, which diverged early from the eukaryotic lineage. Analyses of the first published draft of the trypanosomatid genome sequences failed to recognize orthologs of any of the TFIIIC subunits, suggesting that this transcription factor is absent in these parasites. However, a putative TFIIIC subunit was recently annotated in the databases. Here we characterize this subunit in T. brucei and L. major and demonstrate that it corresponds to Tau95. In silico analyses showed that both proteins possess the typical Tau95 sequences: the DNA binding region and the dimerization domain. As anticipated for a transcription factor, Tau95 localized to the nucleus in insect forms of both parasites. Chromatin immunoprecipitation (ChIP) assays demonstrated that Tau95 binds to tRNA and U2 snRNA genes in T. brucei. Remarkably, by performing tandem affinity purifications we identified orthologs of TFIIIC subunits Tau55, Tau131, and Tau138 in T. brucei and L. major. Thus, contrary to what was assumed, trypanosomatid parasites do possess a TFIIIC complex. Other putative interacting partners of Tau95 were identified in T. brucei and L. major. KEY POINTS: • A four-subunit TFIIIC complex is present in T. brucei and L. major • TbTau95 associates with tRNA and U2 snRNA genes • Putative interacting partners of Tau95 might include some RNAP II regulators.
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Affiliation(s)
- Fabiola Mondragón-Rosas
- Facultad de Estudios Superiores Iztacala, Unidad de Biomedicina, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Luis E Florencio-Martínez
- Facultad de Estudios Superiores Iztacala, Unidad de Biomedicina, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Gino S Villa-Delavequia
- Facultad de Estudios Superiores Iztacala, Unidad de Biomedicina, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Rebeca G Manning-Cela
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN 2508, Ciudad de Mexico, CP 07360, México
| | - Julio C Carrero
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de Mexico, 04510, México
| | - Tomás Nepomuceno-Mejía
- Facultad de Estudios Superiores Iztacala, Unidad de Biomedicina, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México
| | - Santiago Martínez-Calvillo
- Facultad de Estudios Superiores Iztacala, Unidad de Biomedicina, Universidad Nacional Autónoma de México, Av. de los Barrios 1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de México, CP 54090, México.
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2
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Malik Y, Goncalves Silva I, Diazgranados RR, Selman C, Alic N, Tullet JM. Timing of TORC1 inhibition dictates Pol III involvement in Caenorhabditis elegans longevity. Life Sci Alliance 2024; 7:e202402735. [PMID: 38740431 DOI: 10.26508/lsa.202402735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Organismal growth and lifespan are inextricably linked. Target of Rapamycin (TOR) signalling regulates protein production for growth and development, but if reduced, extends lifespan across species. Reduction in the enzyme RNA polymerase III, which transcribes tRNAs and 5S rRNA, also extends longevity. Here, we identify a temporal genetic relationship between TOR and Pol III in Caenorhabditis elegans, showing that they collaborate to regulate progeny production and lifespan. Interestingly, the lifespan interaction between Pol III and TOR is only revealed when TOR signaling is reduced, specifically in adulthood, demonstrating the importance of timing to control TOR regulated developmental versus adult programs. In addition, we show that Pol III acts in C. elegans muscle to promote both longevity and healthspan and that reducing Pol III even in late adulthood is sufficient to extend lifespan. This demonstrates the importance of Pol III for lifespan and age-related health in adult C. elegans.
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Affiliation(s)
- Yasir Malik
- https://ror.org/00xkeyj56 Division of Natural Sciences, School of Biosciences, University of Kent, Canterbury, Kent
| | - Isabel Goncalves Silva
- https://ror.org/00xkeyj56 Division of Natural Sciences, School of Biosciences, University of Kent, Canterbury, Kent
| | - Rene Rivera Diazgranados
- https://ror.org/00xkeyj56 Division of Natural Sciences, School of Biosciences, University of Kent, Canterbury, Kent
| | - Colin Selman
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland
| | - Nazif Alic
- UCL Department of Genetics, Evolution & Environment, Institute of Healthy Ageing, London, UK
| | - Jennifer Ma Tullet
- https://ror.org/00xkeyj56 Division of Natural Sciences, School of Biosciences, University of Kent, Canterbury, Kent
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Rajendra KC, Cheng R, Zhou S, Lizarazo S, Smith D, Van Bortle K. Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.598009. [PMID: 38895345 PMCID: PMC11185800 DOI: 10.1101/2024.06.08.598009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
RNA polymerase (Pol) I, II, and III are most commonly described as having distinct roles in synthesizing ribosomal RNA (rRNA), messenger RNA (mRNA), and specific small noncoding (nc)RNAs, respectively. This delineation of transcriptional responsibilities is not definitive, however, as evidenced by instances of Pol II recruitment to genes conventionally transcribed by Pol III, including the co-transcription of RPPH1 - the catalytic RNA component of RNase P. A comprehensive understanding of the interplay between RNA polymerase complexes remains lacking, however, due to limited comparative analyses for all three enzymes. To address this gap, we applied a uniform framework for quantifying global Pol I, II, and III occupancies that integrates currently available human RNA polymerase ChIP-seq datasets. Occupancy maps are combined with a comprehensive multi-class promoter set that includes protein-coding genes, noncoding genes, and repetitive elements. While our genomic survey appropriately identifies recruitment of Pol I, II, and III to canonical target genes, we unexpectedly discover widespread recruitment of the Pol III machinery to promoters of specific protein-coding genes, supported by colocalization patterns observed for several Pol III-specific subunits. We show that Pol III-occupied Pol II promoters are enriched for small, nascent RNA reads terminating in a run of 4 Ts, a unique hallmark of Pol III transcription termination and evidence of active Pol III activity at these sites. Pol III disruption differentially modulates the expression of Pol III-occupied coding genes, which are functionally enriched for ribosomal proteins and genes broadly linked to unfavorable outcomes in cancer. Our map also identifies additional, currently unannotated genomic elements occupied by Pol III with clear signatures of nascent RNA species that are sensitive to disruption of La (SSB) - a Pol III-related RNA chaperone protein. These findings reshape our current understanding of the interplay between Pols II and III and identify potentially novel small ncRNAs with broad implications for gene regulatory paradigms and RNA biology.
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Affiliation(s)
- K C Rajendra
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruiying Cheng
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Simon Lizarazo
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Duncan Smith
- Department of Biology, New York University, New York, NY
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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4
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Prajapat M, Sala L, Vidigal JA. The small non-coding RNA Vaultrc5 is dispensable to mouse development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596958. [PMID: 38895289 PMCID: PMC11185573 DOI: 10.1101/2024.06.01.596958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Vault RNAs (vRNAs) are evolutionarily conserved small non-coding RNAs transcribed by RNA polymerase lll. Initially described as components of the vault particle, they have since also been described as noncanonical miRNA precursors and as riboregulators of autophagy. As central molecules in these processes, vRNAs have been attributed numerous biological roles including regulation of cell proliferation and survival, response to viral infections, drug resistance, and animal development. Yet, their impact to mammalian physiology remains largely unexplored. To study vault RNAs in vivo, we generated a mouse line with a conditional Vaultrc5 loss of function allele. Because Vaultrc5 is the sole murine vRNA, this allele enables the characterization of the physiological requirements of this conserved class of small regulatory RNAs in mammals. Using this strain, we show that mice constitutively null for Vaultrc5 are viable and histologically normal but have a slight reduction in platelet counts pointing to a potential role for vRNAs in hematopoiesis. This work paves the way for further in vivo characterizations of this abundant but mysterious RNA molecule. Specifically, it enables the study of the biological consequences of constitutive or lineage-specific Vaultrc5 deletion and of the physiological requirements for an intact Vaultrc5 during normal hematopoiesis or in response to cellular stresses such as oncogene expression, viral infection, or drug treatment.
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Affiliation(s)
- Mahendra Prajapat
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Laura Sala
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
| | - Joana A. Vidigal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, The National Institutes of Health, Bethesda, MD, USA
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5
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Struhl K. Non-canonical functions of enhancers: regulation of RNA polymerase III transcription, DNA replication, and V(D)J recombination. Trends Genet 2024; 40:471-479. [PMID: 38643034 PMCID: PMC11152991 DOI: 10.1016/j.tig.2024.04.001] [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: 02/28/2024] [Accepted: 04/02/2024] [Indexed: 04/22/2024]
Abstract
Enhancers are the key regulators of other DNA-based processes by virtue of their unique ability to generate nucleosome-depleted regions in a highly regulated manner. Enhancers regulate cell-type-specific transcription of tRNA genes by RNA polymerase III (Pol III). They are also responsible for the binding of the origin replication complex (ORC) to DNA replication origins, thereby regulating origin utilization, replication timing, and replication-dependent chromosome breaks. Additionally, enhancers regulate V(D)J recombination by increasing access of the recombination-activating gene (RAG) recombinase to target sites and by generating non-coding enhancer RNAs and localized regions of trimethylated histone H3-K4 recognized by the RAG2 PHD domain. Thus, enhancers represent the first step in decoding the genome, and hence they regulate biological processes that, unlike RNA polymerase II (Pol II) transcription, do not have dedicated regulatory proteins.
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Affiliation(s)
- Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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6
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Billi M, De Marinis E, Gentile M, Nervi C, Grignani F. Nuclear miRNAs: Gene Regulation Activities. Int J Mol Sci 2024; 25:6066. [PMID: 38892257 PMCID: PMC11172810 DOI: 10.3390/ijms25116066] [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: 04/22/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs which contribute to the regulation of many physiological and pathological processes. Conventionally, miRNAs perform their activity in the cytoplasm where they regulate gene expression by interacting in a sequence-specific manner with mature messenger RNAs. Recent studies point to the presence of mature miRNAs in the nucleus. This review summarizes current findings regarding the molecular activities of nuclear miRNAs. These molecules can regulate gene expression at the transcriptional level by directly binding DNA on the promoter or the enhancer of regulated genes. miRNAs recruit different protein complexes to these regions, resulting in activation or repression of transcription, through a number of molecular mechanisms. Hematopoiesis is presented as a paradigmatic biological process whereby nuclear miRNAs possess a relevant regulatory role. Nuclear miRNAs can influence gene expression by affecting nuclear mRNA processing and by regulating pri-miRNA maturation, thus impacting the biogenesis of miRNAs themselves. Overall, nuclear miRNAs are biologically active molecules that can be critical for the fine tuning of gene expression and deserve further studies in a number of physiological and pathological conditions.
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Affiliation(s)
- Monia Billi
- General Pathology and Department of Medicine, University of Perugia, 06132 Perugia, Italy;
| | - Elisabetta De Marinis
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Martina Gentile
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Clara Nervi
- Department of Medical-Surgical Sciences and Biotechnologies, University of Rome “La Sapienza”, 04100 Latina, Italy; (E.D.M.); (M.G.); (C.N.)
| | - Francesco Grignani
- General Pathology and Department of Medicine, University of Perugia, 06132 Perugia, Italy;
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7
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Ruan DD, Ruan XL, Wang RL, Lin XF, Zhang YP, Lin B, Li SJ, Wu M, Chen Q, Zhang JH, Cheng Q, Zhang YW, Lin F, Luo JW, Zheng Z, Li YF. Clinical phenotype and genetic function analysis of a family with hypomyelinating leukodystrophy-7 caused by POLR3A mutation. Sci Rep 2024; 14:7638. [PMID: 38561452 PMCID: PMC10985069 DOI: 10.1038/s41598-024-58452-6] [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: 09/06/2023] [Accepted: 03/29/2024] [Indexed: 04/04/2024] Open
Abstract
Hypomyelinating leukodystrophy (HLD) is a rare genetic heterogeneous disease that can affect myelin development in the central nervous system. This study aims to analyze the clinical phenotype and genetic function of a family with HLD-7 caused by POLR3A mutation. The proband (IV6) in this family mainly showed progressive cognitive decline, dentin dysplasia, and hypogonadotropic hypogonadism. Her three old brothers (IV1, IV2, and IV4) also had different degrees of ataxia, dystonia, or dysarthria besides the aforementioned manifestations. Their brain magnetic resonance imaging showed bilateral periventricular white matter atrophy, brain atrophy, and corpus callosum atrophy and thinning. The proband and her two living brothers (IV2 and IV4) were detected to carry a homozygous mutation of the POLR3A (NM_007055.4) gene c. 2300G > T (p.Cys767Phe), and her consanguineous married parents (III1 and III2) were p.Cys767Phe heterozygous carriers. In the constructed POLR3A wild-type and p.Cys767Phe mutant cells, it was seen that overexpression of wild-type POLR3A protein significantly enhanced Pol III transcription of 5S rRNA and tRNA Leu-CAA. However, although the mutant POLR3A protein overexpression was increased compared to the wild-type protein overexpression, it did not show the expected further enhancement of Pol III function. On the contrary, Pol III transcription function was frustrated (POLR3A, BC200, and tRNA Leu-CAA expression decreased), and MBP and 18S rRNA expressions were decreased. This study indicates that the POLR3A p.Cys767Phe variant caused increased expression of mutated POLR3A protein and abnormal expression of Pol III transcripts, and the mutant POLR3A protein function was abnormal.
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Affiliation(s)
- Dan-Dan Ruan
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Xing-Lin Ruan
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Ruo-Li Wang
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
- Fujian Provincial Key Laboratory of Emergency Medicine, Fujian Provincial Institute of Emergency Medicine, Fujian Emergency Medical Center, Fuzhou, 350001, China
| | - Xin-Fu Lin
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
- Pediatrics Department, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Yan-Ping Zhang
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Bin Lin
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Shi-Jie Li
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Min Wu
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Qian Chen
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Jian-Hui Zhang
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
| | - Qiong Cheng
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China
- Department of Neurology, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Yi-Wu Zhang
- Department of Neurology, Youxi County General Hospital, Sanming, 365100, China
| | - Fan Lin
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China.
- Department of Geriatric Medicine, Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, 350001, China.
| | - Jie-Wei Luo
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China.
| | - Zheng Zheng
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China.
- Department of Neurology, Fujian Provincial Hospital, Fuzhou, 350001, China.
| | - Yun-Fei Li
- Department of Traditional Chinese Medicine, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, China.
- Department of Neurology, Fujian Provincial Hospital, Fuzhou, 350001, China.
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8
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Avila-Bonilla RG, Macias S. The molecular language of RNA 5' ends: guardians of RNA identity and immunity. RNA (NEW YORK, N.Y.) 2024; 30:327-336. [PMID: 38325897 PMCID: PMC10946433 DOI: 10.1261/rna.079942.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
RNA caps are deposited at the 5' end of RNA polymerase II transcripts. This modification regulates several steps of gene expression, in addition to marking transcripts as self to enable the innate immune system to distinguish them from uncapped foreign RNAs, including those derived from viruses. Specialized immune sensors, such as RIG-I and IFITs, trigger antiviral responses upon recognition of uncapped cytoplasmic transcripts. Interestingly, uncapped transcripts can also be produced by mammalian hosts. For instance, 5'-triphosphate RNAs are generated by RNA polymerase III transcription, including tRNAs, Alu RNAs, or vault RNAs. These RNAs have emerged as key players of innate immunity, as they can be recognized by the antiviral sensors. Mechanisms that regulate the presence of 5'-triphosphates, such as 5'-end dephosphorylation or RNA editing, prevent immune recognition of endogenous RNAs and excessive inflammation. Here, we provide a comprehensive overview of the complexity of RNA cap structures and 5'-triphosphate RNAs, highlighting their roles in transcript identity, immune surveillance, and disease.
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Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
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9
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Yaghoobi A, Rezaee M, Behnoush AH, Khalaji A, Mafi A, Houjaghan AK, Masoudkabir F, Pahlavan S. Role of long noncoding RNAs in pathological cardiac remodeling after myocardial infarction: An emerging insight into molecular mechanisms and therapeutic potential. Biomed Pharmacother 2024; 172:116248. [PMID: 38325262 DOI: 10.1016/j.biopha.2024.116248] [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: 12/11/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024] Open
Abstract
Myocardial infarction (MI) is the leading cause of heart failure (HF), accounting for high mortality and morbidity worldwide. As a consequence of ischemia/reperfusion injury during MI, multiple cellular processes such as oxidative stress-induced damage, cardiomyocyte death, and inflammatory responses occur. In the next stage, the proliferation and activation of cardiac fibroblasts results in myocardial fibrosis and HF progression. Therefore, developing a novel therapeutic strategy is urgently warranted to restrict the progression of pathological cardiac remodeling. Recently, targeting long non-coding RNAs (lncRNAs) provided a novel insight into treating several disorders. In this regard, numerous investigations have indicated that several lncRNAs could participate in the pathogenesis of MI-induced cardiac remodeling, suggesting their potential therapeutic applications. In this review, we summarized lncRNAs displayed in the pathophysiology of cardiac remodeling after MI, emphasizing molecular mechanisms. Also, we highlighted the possible translational role of lncRNAs as therapeutic targets for this condition and discussed the potential role of exosomes in delivering the lncRNAs involved in post-MI cardiac remodeling.
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Affiliation(s)
- Alireza Yaghoobi
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Malihe Rezaee
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Hossein Behnoush
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Amirmohammad Khalaji
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Farzad Masoudkabir
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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10
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Arimbasseri AG, Shukla A, Pradhan AK, Bhargava P. Increased histone acetylation is the signature of repressed state on the genes transcribed by RNA polymerase III. Gene 2024; 893:147958. [PMID: 37923095 DOI: 10.1016/j.gene.2023.147958] [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: 08/10/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Several covalent modifications are found associated with the transcriptionally active chromatin regions constituted by the genes transcribed by RNA polymerase (pol) II. Pol III-transcribed genes code for the small, stable RNA species, which participate in many cellular processes, essential for survival. Pol III transcription is repressed under most of the stress conditions by its negative regulator Maf1. We found that most of the histone acetylations increase with starvation-induced repression on several genes transcribed by the yeast pol III. On one of these genes, SNR6 (coding for the U6snRNA), a strongly positioned nucleosome in the gene upstream region plays regulatory role under repression. On this nucleosome, the changes in H3K9 and H3K14 acetylations show different dynamics. During repression, acetylation levels on H3K9 show steady increase whereas H3K14 acetylation increases with a peak at 40 min after which levels reduce. Both the levels settle by 2 hr to a level higher than the active state, which revert to normal levels with nutrient repletion. The increase in H3 acetylations is seen in the mutants reported to show reduced SNR6 transcription but not in the maf1Δ cells. This increase on a regulatory nucleosome may be part of the signaling mechanisms, which prepare cells for the stress-related quick repression as well as reactivation. The contrasting association of the histone acetylations with pol II and pol III transcription may be an important consideration to make in research studies focused on drug developments targeting histone modifications.
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Affiliation(s)
| | - Ashutosh Shukla
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Ashis Kumar Pradhan
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Purnima Bhargava
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Tarnaka, Hyderabad 500007, India.
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11
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Sizer RE, Butterfield SP, Hancocks LA, Gato De Sousa L, White RJ. Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III. Cancers (Basel) 2024; 16:481. [PMID: 38339234 PMCID: PMC10854548 DOI: 10.3390/cancers16030481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
In all cases tested, TFIIIB is responsible for recruiting pol III to its genetic templates. In mammalian cells, RB binds TFIIIB and prevents its interactions with both promoter DNA and pol III, thereby suppressing transcription. As TFIIIB is not recruited to its target genes when bound by RB, the mechanism predicts that pol III-dependent templates will not be occupied by RB; this contrasts with the situation at most genes controlled by RB, where it can be tethered by promoter-bound sequence-specific DNA-binding factors such as E2F. Contrary to this prediction, however, ChIP-seq data reveal the presence of RB in multiple cell types and the related protein p130 at many loci that rely on pol III for their expression, including RMRP, RN7SL, and a variety of tRNA genes. The sets of genes targeted varies according to cell type and growth state. In such cases, recruitment of RB and p130 can be explained by binding of E2F1, E2F4 and/or E2F5. Genes transcribed by pol III had not previously been identified as common targets of E2F family members. The data provide evidence that E2F may allow for the selective regulation of specific non-coding RNAs by RB, in addition to its influence on overall pol III output through its interaction with TFIIIB.
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Affiliation(s)
| | | | | | | | - Robert J. White
- Department of Biology, University of York, York YO10 5DD, UK; (R.E.S.)
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12
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Ouyang S, Zhou ZX, Liu HT, Ren Z, Liu H, Deng NH, Tian KJ, Zhou K, Xie HL, Jiang ZS. LncRNA-mediated Modulation of Endothelial Cells: Novel Progress in the Pathogenesis of Coronary Atherosclerotic Disease. Curr Med Chem 2024; 31:1251-1264. [PMID: 36788688 DOI: 10.2174/0929867330666230213100732] [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: 06/13/2022] [Revised: 11/06/2022] [Accepted: 11/17/2022] [Indexed: 02/16/2023]
Abstract
Coronary atherosclerotic disease (CAD) is a common cardiovascular disease and an important cause of death. Moreover, endothelial cells (ECs) injury is an early pathophysiological feature of CAD, and long noncoding RNAs (lncRNAs) can modulate gene expression. Recent studies have shown that lncRNAs are involved in the pathogenesis of CAD, especially by regulating ECs. In this review, we summarize the novel progress of lncRNA-modulated ECs in the pathogenesis of CAD, including ECs proliferation, migration, adhesion, angiogenesis, inflammation, apoptosis, autophagy, and pyroptosis. Thus, as lncRNAs regulate ECs in CAD, lncRNAs will provide ideal and novel targets for the diagnosis and drug therapy of CAD.
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Affiliation(s)
- Shao Ouyang
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
- Key Laboratory of Heart Failure Prevention & Treatment of Hengyang, Department of Cardiovascular Medicine, Hengyang Medical School, The Second Affiliated Hospital, Clinical Medicine Research Center of Arteriosclerotic Disease of Hunan Province, University of South China, Hunan 421001, China
| | - Zhi-Xiang Zhou
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Hui-Ting Liu
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Zhong Ren
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Huan Liu
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Nian-Hua Deng
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Kai-Jiang Tian
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Kun Zhou
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Hai-Lin Xie
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
| | - Zhi-Sheng Jiang
- Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, Institute of Cardiovascular Disease, University of South China, Hengyang 421001, China
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13
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Saadh MJ, Almoyad MAA, Arellano MTC, Maaliw RR, Castillo-Acobo RY, Jalal SS, Gandla K, Obaid M, Abdulwahed AJ, Ibrahem AA, Sârbu I, Juyal A, Lakshmaiya N, Akhavan-Sigari R. Long non-coding RNAs: controversial roles in drug resistance of solid tumors mediated by autophagy. Cancer Chemother Pharmacol 2023; 92:439-453. [PMID: 37768333 DOI: 10.1007/s00280-023-04582-z] [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: 01/19/2023] [Accepted: 08/12/2023] [Indexed: 09/29/2023]
Abstract
Current genome-wide studies have indicated that a great number of long non-coding RNAs (lncRNAs) are transcribed from the human genome and appeared as crucial regulators in a variety of cellular processes. Many studies have displayed a significant function of lncRNAs in the regulation of autophagy. Autophagy is a macromolecular procedure in cells in which intracellular substrates and damaged organelles are broken down and recycled to relieve cell stress resulting from nutritional deprivation, irradiation, hypoxia, and cytotoxic agents. Autophagy can be a double-edged sword and play either a protective or a damaging role in cells depending on its activation status and other cellular situations, and its dysregulation is related to tumorigenesis in various solid tumors. Autophagy induced by various therapies has been shown as a unique mechanism of resistance to anti-cancer drugs. Growing evidence is showing the important role of lncRNAs in modulating drug resistance via the regulation of autophagy in a variety of cancers. The role of lncRNAs in drug resistance of cancers is controversial; they may promote or suppress drug resistance via either activation or inhibition of autophagy. Mechanisms by which lncRNAs regulate autophagy to affect drug resistance are different, mainly mediated by the negative regulation of micro RNAs. In this review, we summarize recent studies that investigated the role of lncRNAs/autophagy axis in drug resistance of different types of solid tumors.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman, 11831, Jordan
- Applied Science Research Center, Applied Science Private University, Amman, 11831, Jordan
| | | | | | - Renato R Maaliw
- College of Engineering, Southern Luzon State University, Lucban, Quezon, Philippines
| | | | - Sarah Salah Jalal
- College of Nursing, National University of Science and Technology, Dhi Qar, Iraq
| | - Kumaraswamy Gandla
- Department of Pharmaceutical Analysis, University of Chaitanya, Hanamkonda, India
| | | | | | - Azher A Ibrahem
- Department of Pharmacy, Al-Zahrawi University College, Karbala, Iraq
| | - Ioan Sârbu
- 2nd Department of Surgery-Pediatric Surgery and Orthopedics, "Grigore T. Popa" University of Medicine and Pharmacy, 700115, Iași, Romania.
| | - Ashima Juyal
- Department of Electronics & Communication Engineering, Uttaranchal Institute of Technology, Uttaranchal University, Dehradun, 248007, India
| | - Natrayan Lakshmaiya
- Department of Mechanical Engineering, Saveetha School of Engineering, SIMATS, Chennai, Tamil Nadu, India
| | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center Tuebingen, Tübingen, Germany
- Department of Health Care Management and Clinical Research, Collegium Humanum Warsaw Management University Warsaw, Warsaw, Poland
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14
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Schindler D, Walker RSK, Jiang S, Brooks AN, Wang Y, Müller CA, Cockram C, Luo Y, García A, Schraivogel D, Mozziconacci J, Pena N, Assari M, Sánchez Olmos MDC, Zhao Y, Ballerini A, Blount BA, Cai J, Ogunlana L, Liu W, Jönsson K, Abramczyk D, Garcia-Ruiz E, Turowski TW, Swidah R, Ellis T, Pan T, Antequera F, Shen Y, Nieduszynski CA, Koszul R, Dai J, Steinmetz LM, Boeke JD, Cai Y. Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell 2023; 186:5237-5253.e22. [PMID: 37944512 DOI: 10.1016/j.cell.2023.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ∼190-kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enables an orthogonal tRNA SCRaMbLE system. Following construction in yeast, we obtained evidence of a potent selective force, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH, and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up opportunities to directly test hypotheses surrounding these essential non-coding RNAs.
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Affiliation(s)
- Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, 35032 Marburg, Germany
| | - Roy S K Walker
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3BF, Scotland; School of Natural Sciences and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Aaron N Brooks
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Yun Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Carolin A Müller
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - Charlotte Cockram
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Yisha Luo
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Alicia García
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Daniel Schraivogel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Julien Mozziconacci
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Noah Pena
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Mahdi Assari
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | - Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Alba Ballerini
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Benjamin A Blount
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Jitong Cai
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Lois Ogunlana
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Wei Liu
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Katarina Jönsson
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Dariusz Abramczyk
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Eva Garcia-Ruiz
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Tomasz W Turowski
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Reem Swidah
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Yue Shen
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK; BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Conrad A Nieduszynski
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics and Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
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15
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Wang Y, Halawani D, Estill M, Ramakrishnan A, Shen L, Friedel RH, Zou H. Aryl hydrocarbon receptor restricts axon regeneration of DRG neurons in response to injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.04.565649. [PMID: 37961567 PMCID: PMC10635160 DOI: 10.1101/2023.11.04.565649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Injured neurons sense environmental cues to balance neural protection and axon regeneration, but the mechanisms are unclear. Here, we unveil aryl hydrocarbon receptor (AhR), a ligand-activated bHLH-PAS transcription factor, as molecular sensor and key regulator of acute stress response at the expense of axon regeneration. We demonstrate responsiveness of DRG sensory neurons to ligand-mediated AhR signaling, which functions to inhibit axon regeneration. Ahr deletion mimics the conditioning lesion in priming DRG to initiate axonogenesis gene programs; upon peripheral axotomy, Ahr ablation suppresses inflammation and stress signaling while augmenting pro-growth pathways. Moreover, comparative transcriptomics revealed signaling interactions between AhR and HIF-1α, two structurally related bHLH-PAS α units that share the dimerization partner Arnt/HIF-1β. Functional assays showed that the growth advantage of AhR-deficient DRG neurons requires HIF-1α; but in the absence of Arnt, DRG neurons can still mount a regenerative response. We further unveil a link between bHLH-PAS transcription factors and DNA hydroxymethylation in response to peripheral axotomy, while neuronal single cell RNA-seq analysis revealed a link of the AhR regulon to RNA polymerase III regulation and integrated stress response (ISR). Altogether, AhR activation favors stress coping and inflammation at the expense of axon regeneration; targeting AhR can enhance nerve repair.
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Affiliation(s)
- Yiqun Wang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Current address: Sport Medicine Center, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Dalia Halawani
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Roland H. Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, USA
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16
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Weigert N, Schweiger AL, Gross J, Matthes M, Corbacioglu S, Sommer G, Heise T. Detection of a 7SL RNA-derived small non-coding RNA using Molecular Beacons in vitro and in cells. Biol Chem 2023; 404:1123-1136. [PMID: 37632732 DOI: 10.1515/hsz-2023-0185] [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: 04/14/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023]
Abstract
Small non-coding RNAs (sncRNA) are involved in many steps of the gene expression cascade and regulate processing and expression of mRNAs by the formation of ribonucleoprotein complexes (RNP) such as the RNA-induced silencing complex (RISC). By analyzing small RNA Seq data sets, we identified a sncRNA annotated as piR-hsa-1254, which is likely derived from the 3'-end of 7SL RNA2 (RN7SL2), herein referred to as snc7SL RNA. The 7SL RNA is an abundant long non-coding RNA polymerase III transcript and serves as structural component of the cytoplasmic signal recognition particle (SRP). To evaluate a potential functional role of snc7SL RNA, we aimed to define its cellular localization by live cell imaging. Therefore, a Molecular Beacon (MB)-based method was established to compare the subcellular localization of snc7SL RNA with its precursor 7SL RNA. We designed and characterized several MBs in vitro and tested those by live cell fluorescence microscopy. Using a multiplex approach, we show that 7SL RNA localizes mainly to the endoplasmic reticulum (ER), as expected for the SRP, whereas snc7SL RNA predominately localizes to the nucleus. This finding suggests a fundamentally different function of 7SL RNA and its derivate snc7SL RNA.
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Affiliation(s)
- Nina Weigert
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Anna-Lena Schweiger
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Jonas Gross
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Marie Matthes
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Selim Corbacioglu
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Gunhild Sommer
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Tilman Heise
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
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17
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Daiß JL, Griesenbeck J, Tschochner H, Engel C. Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation. Biol Chem 2023; 404:1003-1023. [PMID: 37454246 DOI: 10.1515/hsz-2023-0214] [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: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.
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Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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18
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Macintosh J, Perrier S, Pinard M, Tran LT, Guerrero K, Prasad C, Prasad AN, Pastinen T, Thiffault I, Coulombe B, Bernard G. Biallelic pathogenic variants in POLR3D alter tRNA transcription and cause a hypomyelinating leukodystrophy: A case report. Front Neurol 2023; 14:1254140. [PMID: 37915380 PMCID: PMC10616956 DOI: 10.3389/fneur.2023.1254140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
RNA polymerase III-related leukodystrophy (POLR3-related leukodystrophy) is a rare, genetically determined hypomyelinating disease arising from biallelic pathogenic variants in genes encoding subunits of RNA polymerase III (Pol III). Here, we describe the first reported case of POLR3-related leukodystrophy caused by biallelic pathogenic variants in POLR3D, encoding the RPC4 subunit of Pol III. The individual, a female, demonstrated delays in walking and expressive and receptive language as a child and later cognitively plateaued. Additional neurological features included cerebellar signs (e.g., dysarthria, ataxia, and intention tremor) and dysphagia, while non-neurological features included hypodontia, hypogonadotropic hypogonadism, and dysmorphic facial features. Her MRI was notable for diffuse hypomyelination with myelin preservation of early myelinating structures, characteristic of POLR3-related leukodystrophy. Exome sequencing revealed the biallelic variants in POLR3D, a missense variant (c.541C > T, p.P181S) and an intronic splice site variant (c.656-6G > A, p.?). Functional studies of the patient's fibroblasts demonstrated significantly decreased RNA-level expression of POLR3D, along with reduced expression of other Pol III subunit genes. Notably, Pol III transcription was also shown to be aberrant, with a significant decrease in 7SK RNA and several distinct tRNA genes analyzed. Affinity purification coupled to mass spectrometry of the POLR3D p.P181S variant showed normal assembly of Pol III subunits yet altered interaction of Pol III with the PAQosome chaperone complex, indicating the missense variant is likely to alter complex maturation. This work identifies biallelic pathogenic variants in POLR3D as a novel genetic cause of POLR3-related leukodystrophy, expanding the molecular spectrum associated with this disease, and proposes altered tRNA homeostasis as a factor in the underlying biology of this hypomyelinating disorder.
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Affiliation(s)
- Julia Macintosh
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Stefanie Perrier
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Maxime Pinard
- Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Luan T. Tran
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Kether Guerrero
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Chitra Prasad
- Department of Pediatrics, London Health Sciences Center and Western University, London, ON, Canada
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Center, London, ON, Canada
- Children’s Health Research Institute, London, ON, Canada
| | - Asuri N. Prasad
- Department of Pediatrics, London Health Sciences Center and Western University, London, ON, Canada
- Children’s Health Research Institute, London, ON, Canada
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, United States
- University of Missouri Kansas City School of Medicine, Kansas City, MO, United States
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO, United States
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, United States
- University of Missouri Kansas City School of Medicine, Kansas City, MO, United States
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, United States
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
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19
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Szatkowska R, Furmanek E, Kierzek AM, Ludwig C, Adamczyk M. Mitochondrial Metabolism in the Spotlight: Maintaining Balanced RNAP III Activity Ensures Cellular Homeostasis. Int J Mol Sci 2023; 24:14763. [PMID: 37834211 PMCID: PMC10572830 DOI: 10.3390/ijms241914763] [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: 07/20/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
RNA polymerase III (RNAP III) holoenzyme activity and the processing of its products have been linked to several metabolic dysfunctions in lower and higher eukaryotes. Alterations in the activity of RNAP III-driven synthesis of non-coding RNA cause extensive changes in glucose metabolism. Increased RNAP III activity in the S. cerevisiae maf1Δ strain is lethal when grown on a non-fermentable carbon source. This lethal phenotype is suppressed by reducing tRNA synthesis. Neither the cause of the lack of growth nor the underlying molecular mechanism have been deciphered, and this area has been awaiting scientific explanation for a decade. Our previous proteomics data suggested mitochondrial dysfunction in the strain. Using model mutant strains maf1Δ (with increased tRNA abundance) and rpc128-1007 (with reduced tRNA abundance), we collected data showing major changes in the TCA cycle metabolism of the mutants that explain the phenotypic observations. Based on 13C flux data and analysis of TCA enzyme activities, the present study identifies the flux constraints in the mitochondrial metabolic network. The lack of growth is associated with a decrease in TCA cycle activity and downregulation of the flux towards glutamate, aspartate and phosphoenolpyruvate (PEP), the metabolic intermediate feeding the gluconeogenic pathway. rpc128-1007, the strain that is unable to increase tRNA synthesis due to a mutation in the C128 subunit, has increased TCA cycle activity under non-fermentable conditions. To summarize, cells with non-optimal activity of RNAP III undergo substantial adaptation to a new metabolic state, which makes them vulnerable under specific growth conditions. Our results strongly suggest that balanced, non-coding RNA synthesis that is coupled to glucose signaling is a fundamental requirement to sustain a cell's intracellular homeostasis and flexibility under changing growth conditions. The presented results provide insight into the possible role of RNAP III in the mitochondrial metabolism of other cell types.
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Affiliation(s)
- Roza Szatkowska
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
| | - Emil Furmanek
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
| | - Andrzej M. Kierzek
- Certara UK Limited, Sheffield S1 2BJ, UK;
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK;
| | - Malgorzata Adamczyk
- Laboratory of Systems and Synthetic Biology, Chair of Drugs and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland; (R.S.)
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20
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Sachs P, Bergmaier P, Treutwein K, Mermoud JE. The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse. Genes (Basel) 2023; 14:1793. [PMID: 37761933 PMCID: PMC10530723 DOI: 10.3390/genes14091793] [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: 08/23/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
In vertebrates, SMARCAD1 participates in transcriptional regulation, heterochromatin maintenance, DNA repair, and replication. The molecular basis underlying its involvement in these processes is not well understood. We identified the RNA polymerase III general transcription factor TFIIIC as an interaction partner of native SMARCAD1 in mouse and human models using endogenous co-immunoprecipitations. TFIIIC has dual functionality, acting as a general transcription factor and as a genome organizer separating chromatin domains. We found that its partnership with SMARCAD1 is conserved across different mammalian cell types, from somatic to pluripotent cells. Using purified proteins, we confirmed that their interaction is direct. A gene expression analysis suggested that SMARCAD1 is dispensable for TFIIIC function as an RNA polymerase III transcription factor in mouse ESCs. The distribution of TFIIIC and SMARCAD1 in the ESC genome is distinct, and unlike in yeast, SMARCAD1 is not enriched at active tRNA genes. Further analysis of SMARCAD1-binding partners in pluripotent and differentiated mammalian cells reveals that SMARCAD1 associates with several factors that have key regulatory roles in chromatin organization, such as cohesin, laminB, and DDX5. Together, our work suggests for the first time that the SMARCAD1 enzyme participates in genome organization in mammalian nuclei through interactions with architectural proteins.
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Affiliation(s)
- Parysatis Sachs
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
- CMC Development, R&D, Sanofi, 65926 Frankfurt, Germany
| | - Philipp Bergmaier
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
- Global Development Operations, R&D, Merck Healthcare, 64293 Darmstadt, Germany
| | - Katrin Treutwein
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
| | - Jacqueline E. Mermoud
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
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21
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Ghulam Mohyuddin S, Liang Y, Xia Y, Wang M, Zhang H, Li M, Yang Z, A. Karrow N, Mao Y. Identification and Classification of Long Non-Coding RNAs in the Mammary Gland of the Holstein Cow. Int J Mol Sci 2023; 24:13585. [PMID: 37686392 PMCID: PMC10487475 DOI: 10.3390/ijms241713585] [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: 07/03/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
The mammary glands, responsible for milk secretion, are regulated at a local level by various hormones, growth factors, non-coding RNAs, and other elements. Recent research has discovered the presence of lncRNAs in these glands, with suggestions that they may be essential for the maintenance and function of mammary glands. Besides directly controlling the gene and protein expression, lncRNAs are believed to play a significant part in numerous physiological and pathological processes. This study focused on examining the mammary gland tissues of Chinese Holstein cows, to identify and categorize long non-coding RNAs (lncRNAs). The research intended to distinguish lncRNAs in the mammary tissues of Holstein cows and contrast them between lactation and non-lactation periods. In this study, mammary gland tissues were sampled from three Holstein cows in early lactation (n = 3, 30 days postpartum) and non-lactation (n = 3, 315 days postpartum) on a large dairy farm in Jiangsu province. Mammary tissue samples were collected during early lactation and again during non-lactation. In total, we detected 1905 lncRNAs, with 57.3% being 500 bp and 612 intronic lncRNAs. The exon count for lncRNAs varied from 2 to 10. It was observed that 96 lncRNA expressions markedly differed between the two stages, with 83 genes being upregulated and 53 downregulated. Enrichment analysis results revealed that Gene Ontology (GO) analysis was primarily abundant in cellular processes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that target genes were predominantly abundant in metabolic pathways, fatty acid biosynthesis, the immune system, and glycosphingolipid biosynthesis. This study analyzed the expression profile and characteristics of lncRNAs in the mammary gland tissues of Holstein cows during both lactation and non-lactation stages, forming a foundation for further investigation into the functional roles of lncRNAs in Holstein cows throughout lactation.
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Affiliation(s)
- Sahar Ghulam Mohyuddin
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.G.M.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Yan Liang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.G.M.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Yuxin Xia
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.G.M.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Mengqi Wang
- Department of Animal Science, Laval University, Québec, QC G1V-0A6, Canada
| | - Huimin Zhang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.G.M.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Mingxun Li
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.G.M.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Zhangping Yang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.G.M.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Niel A. Karrow
- Center for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G-2W1, Canada
| | - Yongjiang Mao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.G.M.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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22
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Talyzina A, Han Y, Banerjee C, Fishbain S, Reyes A, Vafabakhsh R, He Y. Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation. Mol Cell 2023; 83:2641-2652.e7. [PMID: 37402369 PMCID: PMC10528418 DOI: 10.1016/j.molcel.2023.06.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/02/2023] [Accepted: 06/08/2023] [Indexed: 07/06/2023]
Abstract
RNA polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors TFIIIA, TFIIIC, and TFIIIB. Here, we use cryoelectron microscopy (cryo-EM) to visualize the S. cerevisiae complex of TFIIIA and TFIIIC bound to the promoter. Gene-specific factor TFIIIA interacts with DNA and acts as an adaptor for TFIIIC-promoter interactions. We also visualize DNA binding of TFIIIB subunits, Brf1 and TBP (TATA-box binding protein), which results in the full-length 5S rRNA gene wrapping around the complex. Our smFRET study reveals that the DNA within the complex undergoes both sharp bending and partial dissociation on a slow timescale, consistent with the model predicted from our cryo-EM results. Our findings provide new insights into the transcription initiation complex assembly on the 5S rRNA promoter and allow us to directly compare Pol III and Pol II transcription adaptations.
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Affiliation(s)
- Anna Talyzina
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Yan Han
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Chiranjib Banerjee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Susan Fishbain
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Alexis Reyes
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA.
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23
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Sun Y, Fang Q, Liu W, Liu Y, Zhang C. GANT-61 induces cell cycle resting and autophagy by down-regulating RNAP III signal pathway and tRNA-Gly-CCC synthesis to combate chondrosarcoma. Cell Death Dis 2023; 14:461. [PMID: 37488121 PMCID: PMC10366213 DOI: 10.1038/s41419-023-05926-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 06/17/2023] [Accepted: 06/23/2023] [Indexed: 07/26/2023]
Abstract
Chondrosarcoma is ineffective for conventional radiotherapy and chemotherapy with a poor prognosis. Hedgehog (Hh) signal pathway plays a crucial role in tumor growth and progression, which is constitutive activated in chondrosarcoma. GLI transcription factors as targets for new drugs or interference technology for the treatment of chondrosarcoma are of great significance. In this study, we indicated that the Hedgehog-GLI1 signal pathway is activated in chondrosarcoma, which further enhances the RNAP III signal pathway to mediate endogenous tRNA fragments synthesis. Downstream oncology functions of endogenous tRNA fragments, such as "cell cycle" and "death receptor binding", are involved in malignant chondrosarcoma. The GANT-61, as an inhibitor of GLI1, could inhibit chondrosarcoma tumor growth effectively by inhibiting the RNAP III signal pathway and tRNA-Gly-CCC synthesis in vivo. Induced G2/M cell cycle resting, apoptosis, and autophagy were the main mechanisms for the inhibitory effect of GANT-61 on chondrosarcoma, which correspond with the above-described downstream oncology functions of endogenous tRNA fragments. We also identified the molecular mechanism by which GANT-61-induced autophagy is involved in ULK1 expression and MAPK signaling pathway. Thus, GANT-61 will be an ideal and promising strategy for combating chondrosarcoma.
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Affiliation(s)
- Yifeng Sun
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University &Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong, 250014, PR China
- Department of Surgery, Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
- Department of Surgery, Ulm University Hospital, Ulm University, Ulm, Germany
| | - Qiongxuan Fang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Wei Liu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University &Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong, 250014, PR China
| | - Yi Liu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University &Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong, 250014, PR China
| | - Chunming Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University &Shandong Provincial Qianfoshan Hospital, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong, 250014, PR China.
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24
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Liu D, Lu X, Huang W, Zhuang W. Long non-coding RNAs in non-small cell lung cancer: implications for EGFR-TKI resistance. Front Genet 2023; 14:1222059. [PMID: 37456663 PMCID: PMC10349551 DOI: 10.3389/fgene.2023.1222059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is one of the most common types of malignant tumors as well as the leading cause of cancer-related deaths in the world. The application of epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) has dramatically improved the prognosis of NSCLC patients who harbor EGFR mutations. However, despite an excellent initial response, NSCLC inevitably becomes resistant to EGFR-TKIs, leading to irreversible disease progression. Hence, it is of great significance to shed light on the molecular mechanisms underlying the EGFR-TKI resistance in NSCLC. Long non-coding RNAs (lncRNAs) are critical gene modulators that are able to act as oncogenes or tumor suppressors that modulate tumorigenesis, invasion, and metastasis. Recently, extensive evidence demonstrates that lncRNAs also have a significant function in modulating EGFR-TKI resistance in NSCLC. In this review, we present a comprehensive summary of the lncRNAs involved in EGFR-TKI resistance in NSCLC and focus on their detailed mechanisms of action, including activation of alternative bypass signaling pathways, phenotypic transformation, intercellular communication in the tumor microenvironment, competing endogenous RNAs (ceRNAs) networks, and epigenetic modifications. In addition, we briefly discuss the limitations and the clinical implications of current lncRNAs research in this field.
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Affiliation(s)
- Detian Liu
- Department of Thoracic Surgery, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xiaolin Lu
- The Second Clinical Medical College of Nanchang University, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wentao Huang
- Department of Thoracic Surgery, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wei Zhuang
- Department of Thoracic Surgery, Xiangya Hospital of Central South University, Changsha, Hunan, China
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25
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Naesens L, Haerynck F, Gack MU. The RNA polymerase III-RIG-I axis in antiviral immunity and inflammation. Trends Immunol 2023; 44:435-449. [PMID: 37149405 PMCID: PMC10461603 DOI: 10.1016/j.it.2023.04.002] [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: 01/30/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 05/08/2023]
Abstract
Nucleic acid sensors survey subcellular compartments for atypical or mislocalized RNA or DNA, ultimately triggering innate immune responses. Retinoic acid-inducible gene-I (RIG-I) is part of the family of cytoplasmic RNA receptors that can detect viruses. A growing literature demonstrates that mammalian RNA polymerase III (Pol III) transcribes certain viral or cellular DNA sequences into immunostimulatory RIG-I ligands, which elicits antiviral or inflammatory responses. Dysregulation of the Pol III-RIG-I sensing axis can lead to human diseases including severe viral infection outcomes, autoimmunity, and tumor progression. Here, we summarize the newly emerging role of viral and host-derived Pol III transcripts in immunity and also highlight recent advances in understanding how mammalian cells prevent unwanted immune activation by these RNAs to maintain homeostasis.
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Affiliation(s)
- Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA.
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26
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Shekhar AC, Sun YE, Khoo SK, Lin YC, Malau E, Chang WH, Chen HT. Site-directed biochemical analyses reveal that the switchable C-terminus of Rpc31 contributes to RNA polymerase III transcription initiation. Nucleic Acids Res 2023; 51:4223-4236. [PMID: 36484109 PMCID: PMC10201443 DOI: 10.1093/nar/gkac1163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 08/23/2023] Open
Abstract
Rpc31 is a subunit in the TFIIE-related Rpc82/34/31 heterotrimeric subcomplex of Saccharomyces cerevisiae RNA polymerase III (pol III). Structural analyses of pol III have indicated that the N-terminal region of Rpc31 anchors on Rpc82 and further interacts with the polymerase core and stalk subcomplex. However, structural and functional information for the C-terminal region of Rpc31 is sparse. We conducted a mutational analysis on Rpc31, which uncovered a functional peptide adjacent to the highly conserved Asp-Glu-rich acidic C-terminus. This C-terminal peptide region, termed 'pre-acidic', is important for optimal cell growth, tRNA synthesis, and stable association of Rpc31 in the pre-initiation complex (PIC). Our site-directed photo-cross-linking to map protein interactions within the PIC reveal that this pre-acidic region specifically targets Rpc34 during transcription initiation, but also interacts with the DNA entry surface in free pol III. Thus, we have uncovered a switchable Rpc31 C-terminal region that functions in an initiation-specific protein interaction for pol III transcription.
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Affiliation(s)
| | - Yuan-En Sun
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, R.O.C
| | - Seok-Kooi Khoo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, R.O.C
| | - Yu-Chun Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, R.O.C
| | | | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taiwan, R.O.C
| | - Hung-Ta Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, R.O.C
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27
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Talyzina A, Han Y, Banerjee C, Fishbain S, Reyes A, Vafabakhsh R, He Y. Structural basis of TFIIIC-dependent RNA Polymerase III transcription initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.540967. [PMID: 37292922 PMCID: PMC10245719 DOI: 10.1101/2023.05.16.540967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA Polymerase III (Pol III) is responsible for transcribing 5S ribosomal RNA (5S rRNA), tRNAs, and other short non-coding RNAs. Its recruitment to the 5S rRNA promoter requires transcription factors TFIIIA, TFIIIC, and TFIIIB. Here we use cryo-electron microscopy to visualize the S. cerevisiae complex of TFIIIA and TFIIIC bound to the promoter. Brf1-TBP binding further stabilizes the DNA, resulting in the full-length 5S rRNA gene wrapping around the complex. Our smFRET study reveals that the DNA undergoes both sharp bending and partial dissociation on a slow timescale, consistent with the model predicted from our cryo-EM results. Our findings provide new insights into the mechanism of how the transcription initiation complex assembles on the 5S rRNA promoter, a crucial step in Pol III transcription regulation.
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Affiliation(s)
- Anna Talyzina
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States
| | - Yan Han
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
| | - Chiranjib Banerjee
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
| | - Susan Fishbain
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
| | - Alexis Reyes
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, United States
- Lead contact
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28
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Alalmaie A, Diaf S, Khashan R. Insight into the molecular mechanism of the transposon-encoded type I-F CRISPR-Cas system. J Genet Eng Biotechnol 2023; 21:60. [PMID: 37191877 DOI: 10.1186/s43141-023-00507-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
CRISPR-Cas9 is a popular gene-editing tool that allows researchers to introduce double-strand breaks to edit parts of the genome. CRISPR-Cas9 system is used more than other gene-editing tools because it is simple and easy to customize. However, Cas9 may produce unintended double-strand breaks in DNA, leading to off-target effects. There have been many improvements in the CRISPR-Cas system to control the off-target effect and improve the efficiency. The presence of a nuclease-deficient CRISPR-Cas system in several bacterial Tn7-like transposons inspires researchers to repurpose to direct the insertion of Tn7-like transposons instead of cleaving the target DNA, which will eventually limit the risk of off-target effects. Two transposon-encoded CRISPR-Cas systems have been experimentally confirmed. The first system, found in Tn7 like-transposon (Tn6677), is associated with the variant type I-F CRISPR-Cas system. The second one, found in Tn7 like-transposon (Tn5053), is related to the variant type V-K CRISPR-Cas system. This review describes the molecular and structural mechanisms of DNA targeting by the transposon-encoded type I-F CRISPR-Cas system, from assembly around the CRISPR-RNA (crRNA) to the initiation of transposition.
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Affiliation(s)
- Amnah Alalmaie
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, Saint Joseph University, Philadelphia, PA, 19131, USA
| | - Saousen Diaf
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, Saint Joseph University, Philadelphia, PA, 19131, USA
| | - Raed Khashan
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Sciences, Long Island University, Brooklyn, NY, 11201, USA.
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29
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Lee YS, Lee YS. nc886, an RNA Polymerase III-Transcribed Noncoding RNA Whose Expression Is Dynamic and Regulated by Intriguing Mechanisms. Int J Mol Sci 2023; 24:ijms24108533. [PMID: 37239877 DOI: 10.3390/ijms24108533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/28/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
nc886 is a medium-sized non-coding RNA that is transcribed by RNA polymerase III (Pol III) and plays diverse roles in tumorigenesis, innate immunity, and other cellular processes. Although Pol III-transcribed ncRNAs were previously thought to be expressed constitutively, this concept is evolving, and nc886 is the most notable example. The transcription of nc886 in a cell, as well as in human individuals, is controlled by multiple mechanisms, including its promoter CpG DNA methylation and transcription factor activity. Additionally, the RNA instability of nc886 contributes to its highly variable steady-state expression levels in a given situation. This comprehensive review discusses nc886's variable expression in physiological and pathological conditions and critically examines the regulatory factors that determine its expression levels.
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Affiliation(s)
- Yeon-Su Lee
- Rare Cancer Branch, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
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30
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Mao J, Wei S, Chen Y, Yang Y, Yin T. The proposed role of MSL-lncRNAs in causing sex lability of female poplars. HORTICULTURE RESEARCH 2023; 10:uhad042. [PMID: 37188057 PMCID: PMC10177001 DOI: 10.1093/hr/uhad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/02/2023] [Indexed: 05/17/2023]
Abstract
Labile sex expression is frequently observed in dioecious plants, but the underlying genetic mechanism remains largely unknown. Sex plasticity is also observed in many Populus species. Here we carried out a systematic study on a maleness-promoting gene, MSL, detected in the Populus deltoides genome. Our results showed that both strands of MSL contained multiple cis-activating elements, which generated long non-coding RNAs (lncRNAs) promoting maleness. Although female P. deltoides did not have the male-specific MSL gene, a large number of partial sequences with high sequence similarity to this gene were detected in the female poplar genome. Based on sequence alignment, the MSL sequence could be divided into three partial sequences, and heterologous expression of these partial sequences in Arabidopsis confirmed that they could promote maleness. Since activation of the MSL sequences can only result in female sex lability, we propose that MSL-lncRNAs might play a role in causing sex lability of female poplars.
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Affiliation(s)
| | | | - Yingnan Chen
- State Key Laboratory for Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Breeding of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
| | - Yonghua Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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Saxena S, Das A, Kaila T, Ramakrishna G, Sharma S, Gaikwad K. Genomic survey of high-throughput RNA-Seq data implicates involvement of long intergenic non-coding RNAs (lincRNAs) in cytoplasmic male-sterility and fertility restoration in pigeon pea. Genes Genomics 2023; 45:783-811. [PMID: 37115379 DOI: 10.1007/s13258-023-01383-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/21/2022] [Indexed: 04/29/2023]
Abstract
BACKGROUND Long-intergenic non-coding RNAs (lincRNAs) originate from intergenic regions and have no coding potential. LincRNAs have emerged as key players in the regulation of various biological processes in plant development. Cytoplasmic male-sterility (CMS) in association with restorer-of-fertility (Rf) systems makes it a highly reliable tool for exploring heterosis for producing commercial hybrid seeds. To date, there have been no reports of lincRNAs during pollen development in CMS and fertility restorer lines in pigeon pea. OBJECTIVE Identification of lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines. METHODS We employed a computational approach to identify lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines using RNA-Seq data. RESULTS We predicted a total of 2145 potential lincRNAs of which 966 were observed to be differentially expressed between the sterile and fertile pollen. We identified, 927 cis-regulated and 383 trans-regulated target genes of the lincRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the target genes revealed that these genes were specifically enriched in pathways like pollen and pollen tube development, oxidative phosphorylation, etc. We detected 23 lincRNAs that were co-expressed with 17 pollen-related genes with known functions. Fifty-nine lincRNAs were predicted to be endogenous target mimics (eTMs) for 25 miRNAs, and found to be associated with pollen development. The, lincRNA regulatory networks revealed that different lincRNA-miRNA-mRNA networks might be associated with CMS and fertility restoration. CONCLUSION Thus, this study provides valuable information by highlighting the functions of lincRNAs as regulators during pollen development in pigeon pea and utilization in hybrid seed production.
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Affiliation(s)
- Swati Saxena
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Antara Das
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tanvi Kaila
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - G Ramakrishna
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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Macintosh J, Michell-Robinson M, Chen X, Bernard G. Decreased RNA polymerase III subunit expression leads to defects in oligodendrocyte development. Front Neurosci 2023; 17:1167047. [PMID: 37179550 PMCID: PMC10167296 DOI: 10.3389/fnins.2023.1167047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023] Open
Abstract
Introduction RNA polymerase III (Pol III) is a critical enzymatic complex tasked with the transcription of ubiquitous non-coding RNAs including 5S rRNA and all tRNA genes. Despite the constitutive nature of this enzyme, hypomorphic biallelic pathogenic variants in genes encoding subunits of Pol III lead to tissue-specific features and cause a hypomyelinating leukodystrophy, characterized by a severe and permanent deficit in myelin. The pathophysiological mechanisms in POLR3- related leukodystrophy and specifically, how reduced Pol III function impacts oligodendrocyte development to account for the devastating hypomyelination seen in the disease, remain poorly understood. Methods In this study, we characterize how reducing endogenous transcript levels of leukodystrophy-associated Pol III subunits affects oligodendrocyte maturation at the level of their migration, proliferation, differentiation, and myelination. Results Our results show that decreasing Pol III expression altered the proliferation rate of oligodendrocyte precursor cells but had no impact on migration. Additionally, reducing Pol III activity impaired the differentiation of these precursor cells into mature oligodendrocytes, evident at both the level of OL-lineage marker expression and on morphological assessment, with Pol III knockdown cells displaying a drastically more immature branching complexity. Myelination was hindered in the Pol III knockdown cells, as determined in both organotypic shiverer slice cultures and co-cultures with nanofibers. Analysis of Pol III transcriptional activity revealed a decrease in the expression of distinct tRNAs, which was significant in the siPolr3a condition. Discussion In turn, our findings provide insight into the role of Pol III in oligodendrocyte development and shed light on the pathophysiological mechanisms of hypomyelination in POLR3-related leukodystrophy.
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Affiliation(s)
- Julia Macintosh
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Mackenzie Michell-Robinson
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Xiaoru Chen
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada
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Stentenbach M, Ermer JA, Rudler DL, Perks KL, Raven SA, Lee RG, McCubbin T, Marcellin E, Siira SJ, Rackham O, Filipovska A. Multi-omic profiling reveals an RNA processing rheostat that predisposes to prostate cancer. EMBO Mol Med 2023:e17463. [PMID: 37093546 DOI: 10.15252/emmm.202317463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Prostate cancer is the most commonly diagnosed malignancy and the third leading cause of cancer deaths. GWAS have identified variants associated with prostate cancer susceptibility; however, mechanistic and functional validation of these mutations is lacking. We used CRISPR-Cas9 genome editing to introduce a missense variant identified in the ELAC2 gene, which encodes a dually localised nuclear and mitochondrial RNA processing enzyme, into the mouse Elac2 gene as well as to generate a prostate-specific knockout of Elac2. These mutations caused enlargement and inflammation of the prostate and nodule formation. The Elac2 variant or knockout mice on the background of the transgenic adenocarcinoma of the mouse prostate (TRAMP) model show that Elac2 mutation with a secondary genetic insult exacerbated the onset and progression of prostate cancer. Multiomic profiling revealed defects in energy metabolism that activated proinflammatory and tumorigenic pathways as a consequence of impaired noncoding RNA processing and reduced protein synthesis. Our physiologically relevant models show that the ELAC2 variant is a predisposing factor for prostate cancer and identify changes that underlie the pathogenesis of this cancer.
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Affiliation(s)
- Maike Stentenbach
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Judith A Ermer
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Danielle L Rudler
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Kara L Perks
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Samuel A Raven
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Richard G Lee
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
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Stasenko DV, Tatosyan KA, Borodulina OR, Kramerov DA. Nucleotide Context Can Modulate Promoter Strength in Genes Transcribed by RNA Polymerase III. Genes (Basel) 2023; 14:genes14040802. [PMID: 37107560 PMCID: PMC10137851 DOI: 10.3390/genes14040802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
The small nuclear RNAs 4.5SH and 4.5SI were characterized only in mouse-like rodents; their genes originate from 7SL RNA and tRNA, respectively. Similar to many genes transcribed by RNA polymerase III (pol III), the genes of 4.5SH and 4.5SI RNAs include boxes A and B, forming an intergenic pol III-directed promoter. In addition, their 5′-flanking sequences have TATA-like boxes at position −31/−24, also required for efficient transcription. The patterns of the three boxes notably differ in the 4.5SH and 4.5SI RNA genes. The A, B, and TATA-like boxes were replaced in the 4.5SH RNA gene with the corresponding boxes in the 4.5SI RNA gene to evaluate their effect on the transcription of transfected constructs in HeLa cells. Simultaneous replacement of all three boxes decreased the transcription level by 40%, which indicates decreased promoter activity in a foreign gene. We developed a new approach to compare the promoter strength based on the competition of two co-transfected gene constructs when the proportion between the constructs modulates their relative activity. This method demonstrated that the promoter activity of 4.5SI is 12 times that of 4.5SH. Unexpectedly, the replacement of all three boxes of the weak 4.5SH promoter with those of the strong 4.5SI gene significantly reduced, rather than enhanced, the promoter activity. Thus, the strength of a pol III-directed promoter can depend on the nucleotide environment of the gene.
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Affiliation(s)
- Danil V Stasenko
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Karina A Tatosyan
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga R Borodulina
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dmitri A Kramerov
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Moon B, Kim M, Kim HJ, Cho JS, Son HJ, Lim BC, Kim KJ, Chae JH, Kim SY. Biallelic POLR3A variants cause Wiedemann-Rautenstrauch syndrome with atypical brain involvement. Clin Exp Pediatr 2023; 66:142-144. [PMID: 36596744 PMCID: PMC9989718 DOI: 10.3345/cep.2022.01144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/07/2022] [Indexed: 12/31/2022] Open
Affiliation(s)
- Byungseung Moon
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Minhye Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Hye Jin Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Jae So Cho
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Hey Joon Son
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Ki Joong Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Jong Hee Chae
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea.,Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
| | - Soo Yeon Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea.,Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
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Watt KE, Macintosh J, Bernard G, Trainor PA. RNA Polymerases I and III in development and disease. Semin Cell Dev Biol 2023; 136:49-63. [PMID: 35422389 PMCID: PMC9550887 DOI: 10.1016/j.semcdb.2022.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/18/2022]
Abstract
Ribosomes are macromolecular machines that are globally required for the translation of all proteins in all cells. Ribosome biogenesis, which is essential for cell growth, proliferation and survival, commences with transcription of a variety of RNAs by RNA Polymerases I and III. RNA Polymerase I (Pol I) transcribes ribosomal RNA (rRNA), while RNA Polymerase III (Pol III) transcribes 5S ribosomal RNA and transfer RNAs (tRNA) in addition to a wide variety of small non-coding RNAs. Interestingly, despite their global importance, disruptions in Pol I and Pol III function result in tissue-specific developmental disorders, with craniofacial anomalies and leukodystrophy/neurodegenerative disease being among the most prevalent. Furthermore, pathogenic variants in genes encoding subunits shared between Pol I and Pol III give rise to distinct syndromes depending on whether Pol I or Pol III function is disrupted. In this review, we discuss the global roles of Pol I and III transcription, the consequences of disruptions in Pol I and III transcription, disorders arising from pathogenic variants in Pol I and Pol III subunits, and mechanisms underpinning their tissue-specific phenotypes.
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Affiliation(s)
- Kristin En Watt
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Julia Macintosh
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, QC, Canada; Departments of Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada; Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada.
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy & Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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Vezzoli M, de Llobet Cucalon LI, Di Vona C, Morselli M, Montanini B, de la Luna S, Teichmann M, Dieci G, Ferrari R. TFIIIC as a Potential Epigenetic Modulator of Histone Acetylation in Human Stem Cells. Int J Mol Sci 2023; 24:ijms24043624. [PMID: 36835038 PMCID: PMC9961906 DOI: 10.3390/ijms24043624] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Regulation of histone acetylation dictates patterns of gene expression and hence cell identity. Due to their clinical relevance in cancer biology, understanding how human embryonic stem cells (hESCs) regulate their genomic patterns of histone acetylation is critical, but it remains largely to be investigated. Here, we provide evidence that acetylation of histone H3 lysine-18 (H3K18ac) and lysine-27 (H3K27ac) is only partially established by p300 in stem cells, while it represents the main histone acetyltransferase (HAT) for these marks in somatic cells. Our analysis reveals that whereas p300 marginally associated with H3K18ac and H3K27ac in hESCs, it largely overlapped with these histone marks upon differentiation. Interestingly, we show that H3K18ac is found at "stemness" genes enriched in RNA polymerase III transcription factor C (TFIIIC) in hESCs, whilst lacking p300. Moreover, TFIIIC was also found in the vicinity of genes involved in neuronal biology, although devoid of H3K18ac. Our data suggest a more complex pattern of HATs responsible for histone acetylations in hESCs than previously considered, suggesting a putative role for H3K18ac and TFIIIC in regulating "stemness" genes as well as genes associated with neuronal differentiation of hESCs. The results break ground for possible new paradigms for genome acetylation in hESCs that could lead to new avenues for therapeutic intervention in cancer and developmental diseases.
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Affiliation(s)
- Marco Vezzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | | | - Chiara Di Vona
- Genome Biology Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), 08003 Barcelona, Spain
| | - Marco Morselli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Barbara Montanini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Susana de la Luna
- Genome Biology Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Martin Teichmann
- Université de Bordeaux INSERM U1312 (Bordeaux Institute of Oncology) 146, rue Léo Saignat, 33076 Bordeaux, France
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
- Correspondence:
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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 2023; 24:414-429. [PMID: 36732602 DOI: 10.1038/s41580-022-00573-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/04/2023]
Abstract
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.
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Archaea/eukaryote-specific ribosomal proteins - guardians of a complex structure. Comput Struct Biotechnol J 2023; 21:1249-1261. [PMID: 36817958 PMCID: PMC9932298 DOI: 10.1016/j.csbj.2023.01.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/09/2023] [Accepted: 01/26/2023] [Indexed: 01/29/2023] Open
Abstract
In three domains of life, proteins are synthesized by large ribonucleoprotein particles called ribosomes. All ribosomes are composed of ribosomal RNAs (rRNA) and numerous ribosomal proteins (r-protein). The three-dimensional shape of ribosomes is mainly defined by a tertiary structure of rRNAs. In addition, rRNAs have a major role in decoding the information carried by messenger RNAs and catalyzing the peptide bond formation. R-proteins are essential for shaping the network of interactions that contribute to a various aspects of the protein synthesis machinery, including assembly of ribosomes and interaction of ribosomal subunits. Structural studies have revealed that many key components of ribosomes are conserved in all life domains. Besides the core structure, ribosomes contain domain-specific structural features that include additional r-proteins and extensions of rRNA and r-proteins. This review focuses specifically on those r-proteins that are found only in archaeal and eukaryotic ribosomes. The role of these archaea/eukaryote specific r-proteins in stabilizing the ribosome structure is discussed. Several examples illustrate their functions in the formation of the internal network of ribosomal subunits and interactions between the ribosomal subunits. In addition, the significance of these r-proteins in ribosome biogenesis and protein synthesis is highlighted.
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MoMaf1 Mediates Vegetative Growth, Conidiogenesis, and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae. J Fungi (Basel) 2023; 9:jof9010106. [PMID: 36675927 PMCID: PMC9861366 DOI: 10.3390/jof9010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
In eukaryotes, Maf1 is an essential and specific negative regulator of RNA polymerase (Pol) III. Pol III, which synthesizes 5S RNA and transfer RNAs (tRNAs), is suppressed by Maf1 under the conditions of nutrient starvation or environmental stress. Here, we identified M. oryzae MoMaf1, a homolog of ScMaf1 in budding yeast. A heterogeneous complementation assay revealed that MoMaf1 restored growth defects in the ΔScmaf1 mutant under SDS stress. Destruction of MoMAF1 elevated 5S rRNA content and increased sensitivity to cell wall agents. Moreover, the ΔMomaf1 mutant exhibited reduced vegetative growth, conidiogenesis, and pathogenicity. Interestingly, we found that MoMaf1 underwent nuclear-cytoplasmic shuffling, through which MoMaf1 accumulated in nuclei under nutrient deficiency or upon the interaction of M. oryzae with rice. Therefore, this study can help to elucidate the pathogenic molecular mechanism of M. oryzae.
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Kumar D, Sahoo SS, Chauss D, Kazemian M, Afzali B. Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations. J Autoimmun 2023; 134:102982. [PMID: 36592512 PMCID: PMC9908861 DOI: 10.1016/j.jaut.2022.102982] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/02/2023]
Abstract
Immune cell function is critically dependent on precise control over transcriptional output from the genome. In this respect, integration of environmental signals that regulate gene expression, specifically by transcription factors, enhancer DNA elements, genome topography and non-coding RNAs (ncRNAs), are key components. The first three have been extensively investigated. Even though non-coding RNAs represent the vast majority of cellular RNA species, this class of RNA remains historically understudied. This is partly because of a lag in technological and bioinformatic innovations specifically capable of identifying and accurately measuring their expression. Nevertheless, recent progress in this domain has enabled a profusion of publications identifying novel sub-types of ncRNAs and studies directly addressing the function of ncRNAs in human health and disease. Many ncRNAs, including circular and enhancer RNAs, have now been demonstrated to play key functions in the regulation of immune cells and to show associations with immune-mediated diseases. Some ncRNAs may function as biomarkers of disease, aiding in diagnostics and in estimating response to treatment, while others may play a direct role in the pathogenesis of disease. Importantly, some are relatively stable and are amenable to therapeutic targeting, for example through gene therapy. Here, we provide an overview of ncRNAs and review technological advances that enable their study and hold substantial promise for the future. We provide context-specific examples by examining the associations of ncRNAs with four prototypical human autoimmune diseases, specifically rheumatoid arthritis, psoriasis, inflammatory bowel disease and multiple sclerosis. We anticipate that the utility and mechanistic roles of these ncRNAs in autoimmunity will be further elucidated in the near future.
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Affiliation(s)
- Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Subhransu Sekhar Sahoo
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
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42
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Hao Y, Xie B, Fu X, Xu R, Yang Y. New Insights into lncRNAs in Aβ Cascade Hypothesis of Alzheimer's Disease. Biomolecules 2022; 12:biom12121802. [PMID: 36551230 PMCID: PMC9775548 DOI: 10.3390/biom12121802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
Alzheimer's disease (AD) is the most common type of dementia, but its pathogenesis is not fully understood, and effective drugs to treat or reverse the progression of the disease are lacking. Long noncoding RNAs (lncRNAs) are abnormally expressed and deregulated in AD and are closely related to the occurrence and development of AD. In addition, the high tissue specificity and spatiotemporal specificity make lncRNAs particularly attractive as diagnostic biomarkers and specific therapeutic targets. Therefore, an in-depth understanding of the regulatory mechanisms of lncRNAs in AD is essential for developing new treatment strategies. In this review, we discuss the unique regulatory functions of lncRNAs in AD, ranging from Aβ production to clearance, with a focus on their interaction with critical molecules. Additionally, we highlight the advantages and challenges of using lncRNAs as biomarkers for diagnosis or therapeutic targets in AD and present future perspectives in clinical practice.
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Affiliation(s)
- Yitong Hao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Bo Xie
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Xiaoshu Fu
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Rong Xu
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun 130021, China
| | - Yu Yang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
- Correspondence:
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43
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Liu S, Li X, Liu X, Wang J, Li L, Kong D. RNA polymerase III directly participates in DNA homologous recombination. Trends Cell Biol 2022; 32:988-995. [PMID: 35811227 DOI: 10.1016/j.tcb.2022.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/05/2022] [Accepted: 06/14/2022] [Indexed: 01/21/2023]
Abstract
A recent study showed that RNA transcription is directly involved in DNA homologous recombination (HR). The first step in HR is end resection, which degrades a few kilobases or more from the 5'-end strand at DNA breaks, but the 3'-end strand remains strictly intact. Such protection of the 3'-end strand is achieved by the transient formation of an RNA-DNA hybrid structure. The RNA strand in the hybrid is newly synthesized by RNA polymerase III. The revelation of the existence of an RNA-DNA hybrid intermediate should further help resolve several long-standing questions of HR. In this article, we also put forward our views on some controversial issues related to RNA-DNA hybrids, RNA polymerases, and the protection of 3'-end strands.
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Affiliation(s)
- Sijie Liu
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.
| | - Xizhou Li
- Department of Breast and Thyroid Surgery, Changhai Hospital, The Naval Military Medical University, Shanghai, China
| | - Xiaoqin Liu
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China; Institute of Brain Science, Shanxi Datong University, Datong 037009, China
| | - Jingna Wang
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Lingyan Li
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Daochun Kong
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.
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44
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The POLR3G Subunit of Human RNA Polymerase III Regulates Tumorigenesis and Metastasis in Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14235732. [PMID: 36497214 PMCID: PMC9735567 DOI: 10.3390/cancers14235732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
RNA polymerase (Pol) III transcribes short untranslated RNAs that contribute to the regulation of gene expression. Two isoforms of human Pol III have been described that differ by the presence of the POLR3G/RPC32α or POLR3GL/RPC32β subunits. POLR3G was found to be expressed in embryonic stem cells and at least a subset of transformed cells, whereas POLR3GL shows a ubiquitous expression pattern. Here, we demonstrate that POLR3G is specifically overexpressed in clinical samples of triple-negative breast cancer (TNBC) but not in other molecular subtypes of breast cancer. POLR3G KO in the MDA-MB231 TNBC cell line dramatically reduces anchorage-independent growth and invasive capabilities in vitro. In addition, the POLR3G KO impairs tumor growth and metastasis formation of orthotopic xenografts in mice. Moreover, KO of POLR3G induces expression of the pioneer transcription factor FOXA1 and androgen receptor. In contrast, the POLR3G KO neither alters proliferation nor the expression of epithelial-mesenchymal transition marker genes. These data demonstrate that POLR3G expression is required for TNBC tumor growth, invasiveness and dissemination and that its deletion affects triple-negative breast cancer-specific gene expression.
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45
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Jacobs RQ, Carter ZI, Lucius AL, Schneider DA. Uncovering the mechanisms of transcription elongation by eukaryotic RNA polymerases I, II, and III. iScience 2022; 25:105306. [PMID: 36304104 PMCID: PMC9593817 DOI: 10.1016/j.isci.2022.105306] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/16/2022] [Accepted: 10/03/2022] [Indexed: 11/01/2022] Open
Abstract
Eukaryotes express three nuclear RNA polymerases (Pols I, II, and III) that are essential for cell survival. Despite extensive investigation of the three Pols, significant knowledge gaps regarding their biochemical properties remain because each Pol has been evaluated independently under disparate experimental conditions and methodologies. To advance our understanding of the Pols, we employed identical in vitro transcription assays for direct comparison of their elongation rates, elongation complex (EC) stabilities, and fidelities. Pol I is the fastest, most likely to misincorporate, forms the least stable EC, and is most sensitive to alterations in reaction buffers. Pol II is the slowest of the Pols, forms the most stable EC, and negligibly misincorporated an incorrect nucleotide. The enzymatic properties of Pol III were intermediate between Pols I and II in all assays examined. These results reveal unique enzymatic characteristics of the Pols that provide new insights into their evolutionary divergence.
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Affiliation(s)
- Ruth Q. Jacobs
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zachariah I. Carter
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aaron L. Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Abstract
tRNAs are key adaptor molecules that decipher the genetic code during translation of mRNAs in protein synthesis. In contrast to the traditional view of tRNAs as ubiquitously expressed housekeeping molecules, awareness is now growing that tRNA-encoding genes display tissue-specific and cell type-specific patterns of expression, and that tRNA gene expression and function are both dynamically regulated by post-transcriptional RNA modifications. Moreover, dysregulation of tRNAs, mediated by alterations in either their abundance or function, can have deleterious consequences that contribute to several distinct human diseases, including neurological disorders and cancer. Accumulating evidence shows that reprogramming of mRNA translation through altered tRNA activity can drive pathological processes in a codon-dependent manner. This Review considers the emerging evidence in support of the precise control of functional tRNA levels as an important regulatory mechanism that coordinates mRNA translation and protein expression in physiological cell homeostasis, and highlights key examples of human diseases that are linked directly to tRNA dysregulation.
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Affiliation(s)
- Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Elisabeth Siegal
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Harvard Initiative for RNA Medicine, Harvard University, Boston, MA, USA.
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Babel N, Hugo C, Westhoff TH. Vaccination in patients with kidney failure: lessons from COVID-19. Nat Rev Nephrol 2022; 18:708-723. [PMID: 35999285 PMCID: PMC9397175 DOI: 10.1038/s41581-022-00617-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2022] [Indexed: 02/06/2023]
Abstract
Infection is the second leading cause of death in patients with chronic kidney disease (CKD). Adequate humoral (antibody) and cellular (T cell-driven) immunity are required to minimize pathogen entry and promote pathogen clearance to enable infection control. Vaccination can generate cellular and humoral immunity against specific pathogens and is used to prevent many life-threatening infectious diseases. However, vaccination efficacy is diminished in patients with CKD. Premature ageing of the immune system and chronic systemic low-grade inflammation are the main causes of immune alteration in these patients. In the case of SARS-CoV-2 infection, COVID-19 can have considerable detrimental effects in patients with CKD, especially in those with kidney failure. COVID-19 prevention through successful vaccination is therefore paramount in this vulnerable population. Although patients receiving dialysis have seroconversion rates comparable to those of patients with normal kidney function, most kidney transplant recipients could not generate humoral immunity after two doses of the COVID-19 vaccine. Importantly, some patients who were not able to produce antibodies still had a detectable vaccine-specific T cell response, which might be sufficient to prevent severe COVID-19. Correlates of protection against SARS-CoV-2 have not been established for patients with kidney failure, but they are urgently needed to enable personalized vaccination regimens.
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Affiliation(s)
- Nina Babel
- Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
- Center for Translational Medicine and Immune Diagnostics Laboratory, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Center for Advanced Therapies (BeCAT) and Berlin Institute of Health, Berlin, Germany.
| | - Christian Hugo
- Medizinische Klinik und Poliklinik III, Universitätsklinikum, Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Timm H Westhoff
- Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
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48
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Vago R, Radano G, Zocco D, Zarovni N. Urine stabilization and normalization strategies favor unbiased analysis of urinary EV content. Sci Rep 2022; 12:17663. [PMID: 36271135 PMCID: PMC9587215 DOI: 10.1038/s41598-022-22577-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/17/2022] [Indexed: 01/18/2023] Open
Abstract
Urine features an ideal source of non-invasive diagnostic markers. Some intrinsic and methodological issues still pose barriers to its full potential as liquid biopsy substrate. Unlike blood, urine concentration varies with nutrition, hydration and environmental factors. Urine is enriched with EVs from urinary-genital tract, while its conservation, purification and normalization can introduce bias in analysis of EV subsets in inter-and intra-individual comparisons. The present study evaluated the methods that decrease such biases such as appropriate and feasible urine storage, optimal single-step EV purification method for recovery of proteins and RNAs from small urine volumes and a normalization method for quantitative analysis of urine EV RNAs. Ultracentrifugation, chemical precipitation and immuno-affinity were used to isolate EVs from healthy donors' urine that was stored frozen or at room temperature for up to 6 months. Multiple urine biochemical and EV parameters, including particle count and protein content, were compared across urine samples. To this purpose nanoparticle tracking analysis (NTA) and protein assessment by BCA, ELISA and WB assays were performed. These measurements were correlated with relative abundances of selected EV mRNAs and miRNAs assessed by RT-PCR and ranked for the ability to reflect and correct for EV content variations in longitudinal urine samples. All purification methods enabled recovery and downstream analysis of EVs from as few as 1 ml of urine. Our findings highlight long term stability of EV RNAs upon urine storage at RT as well as excellent correlation of EV content in urine with some routinely measured biochemical features, such as total urine protein and albumin, but not creatinine most conventionally used for urine normalization. Comparative evaluation of mRNA and miRNAs in EV isolates revealed specific RNAs, in particular RNY4 and small miRNA panel, levels of which well reflected the inter-sample EV variation and therefore useful as possible post-analytical normalizers of EV RNA content. We describe some realistic urine processing and normalization solutions for unbiased readout of EV biomarker studies and routine clinical sampling and diagnostics providing the input for design of larger validation studies employing urine EVs as biomarkers for particular conditions and diseases.
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Affiliation(s)
- Riccardo Vago
- grid.18887.3e0000000417581884Urological Research Institute, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy ,grid.15496.3f0000 0001 0439 0892Università Vita-Salute San Raffaele, 20132 Milan, Italy
| | | | | | - Natasa Zarovni
- Exosomics S.p.A, 53100 Siena, Italy ,HansaBiomed Life Sciences OU, Tallinn, Estonia
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49
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Oyelami FO, Usman T, Suravajhala P, Ali N, Do DN. Emerging Roles of Noncoding RNAs in Bovine Mastitis Diseases. Pathogens 2022; 11:pathogens11091009. [PMID: 36145441 PMCID: PMC9501195 DOI: 10.3390/pathogens11091009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are an abundant class of RNA with varying nucleotide lengths. They have been shown to have great potential in eutherians/human disease diagnosis and treatments and are now gaining more importance for the improvement of diseases in livestock. To date, thousands of ncRNAs have been discovered in the bovine genome and the continuous advancement in deep sequencing technologies and various bioinformatics tools has enabled the elucidation of their roles in bovine health. Among farm animals' diseases, mastitis, a common inflammatory disease in cattle, has caused devastating economic losses to dairy farmers over the last few decades. Here, we summarize the biology of bovine mastitis and comprehensively discuss the roles of ncRNAs in different types of mastitis infection. Based on our findings and relevant literature, we highlighted various evidence of ncRNA roles in mastitis. Different approaches (in vivo versus in vitro) for exploring ncRNA roles in mastitis are emphasized. More particularly, the potential applications of emerging genome editing technologies, as well as integrated omics platforms for ncRNA studies and implications for mastitis are presented.
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Affiliation(s)
- Favour Oluwapelumi Oyelami
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Tahir Usman
- College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, Kerala, India
| | - Nawab Ali
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Duy N. Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Correspondence: ; Tel.: +1-9029578789
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50
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Santana JF, Collins GS, Parida M, Luse DS, Price D. Differential dependencies of human RNA polymerase II promoters on TBP, TAF1, TFIIB and XPB. Nucleic Acids Res 2022; 50:9127-9148. [PMID: 35947745 PMCID: PMC9458433 DOI: 10.1093/nar/gkac678] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/08/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
The effects of rapid acute depletion of components of RNA polymerase II (Pol II) general transcription factors (GTFs) that are thought to be critical for formation of preinitiation complexes (PICs) and initiation in vitro were quantified in HAP1 cells using precision nuclear run-on sequencing (PRO-Seq). The average dependencies for each factor across >70 000 promoters varied widely even though levels of depletions were similar. Some of the effects could be attributed to the presence or absence of core promoter elements such as the upstream TBP-specificity motif or downstream G-rich sequences, but some dependencies anti-correlated with such sequences. While depletion of TBP had a large effect on most Pol III promoters only a small fraction of Pol II promoters were similarly affected. TFIIB depletion had the largest general effect on Pol II and also correlated with apparent termination defects downstream of genes. Our results demonstrate that promoter activity is combinatorially influenced by recruitment of TFIID and sequence-specific transcription factors. They also suggest that interaction of the preinitiation complex (PIC) with nucleosomes can affect activity and that recruitment of TFIID containing TBP only plays a positive role at a subset of promoters.
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Affiliation(s)
- Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Geoffrey S Collins
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Mrutyunjaya Parida
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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