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Catalanotto C, Barbato C, Cogoni C, Benelli D. The RNA-Binding Function of Ribosomal Proteins and Ribosome Biogenesis Factors in Human Health and Disease. Biomedicines 2023; 11:2969. [PMID: 38001969 PMCID: PMC10669870 DOI: 10.3390/biomedicines11112969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The ribosome is a macromolecular complex composed of RNA and proteins that interact through an integrated and interconnected network to preserve its ancient core activities. In this review, we emphasize the pivotal role played by RNA-binding proteins as a driving force in the evolution of the current form of the ribosome, underscoring their importance in ensuring accurate protein synthesis. This category of proteins includes both ribosomal proteins and ribosome biogenesis factors. Impairment of their RNA-binding activity can also lead to ribosomopathies, which is a group of disorders characterized by defects in ribosome biogenesis that are detrimental to protein synthesis and cellular homeostasis. A comprehensive understanding of these intricate processes is essential for elucidating the mechanisms underlying the resulting diseases and advancing potential therapeutic interventions.
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Affiliation(s)
- Caterina Catalanotto
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
| | - Christian Barbato
- National Research Council (CNR), Department of Sense Organs DOS, Institute of Biochemistry and Cell Biology (IBBC), Sapienza University of Rome, 00185 Rome, Italy;
| | - Carlo Cogoni
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
| | - Dario Benelli
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (C.C.); (C.C.)
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Noguera NI, Travaglini S, Scalea S, Catalanotto C, Reale A, Zampieri M, Zaza A, Ricciardi MR, Angelini DF, Tafuri A, Ottone T, Voso MT, Zardo G. YY1 Knockdown Relieves the Differentiation Block and Restores Apoptosis in AML Cells. Cancers (Basel) 2023; 15:4010. [PMID: 37568827 PMCID: PMC10417667 DOI: 10.3390/cancers15154010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
In this study we analyzed the expression of Yin and Yang 1 protein (YY1), a member of the noncanonical PcG complexes, in AML patient samples and AML cell lines and the effect of YY1 downregulation on the AML differentiation block. Our results show that YY1 is significantly overexpressed in AML patient samples and AML cell lines and that YY1 knockdown relieves the differentiation block. YY1 downregulation in two AML cell lines (HL-60 and OCI-AML3) and one AML patient sample restored the expression of members of the CEBP protein family, increased the expression of extrinsic growth factors/receptors and surface antigenic markers, induced morphological cell characteristics typical of myeloid differentiation, and sensitized cells to retinoic acid treatment and to apoptosis. Overall, our data show that YY1 is not a secondary regulator of myeloid differentiation but that, if overexpressed, it can play a predominant role in myeloid differentiation block.
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Affiliation(s)
- Nelida Ines Noguera
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Serena Travaglini
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Stefania Scalea
- Department of Experimental Medicine, Sapienza University, 00185 Rome, Italy;
| | - Caterina Catalanotto
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (C.C.); (A.R.); (M.Z.)
| | - Anna Reale
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (C.C.); (A.R.); (M.Z.)
| | - Michele Zampieri
- Department of Molecular Medicine, Sapienza University, 00185 Rome, Italy; (C.C.); (A.R.); (M.Z.)
| | - Alessandra Zaza
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University, 00185 Rome, Italy
| | - Maria Rosaria Ricciardi
- Department of Clinical and Molecular Medicine, Sapienza University, 00185 Rome, Italy; (M.R.R.); (A.T.)
| | | | - Agostino Tafuri
- Department of Clinical and Molecular Medicine, Sapienza University, 00185 Rome, Italy; (M.R.R.); (A.T.)
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy; (S.T.); (T.O.); (M.T.V.)
- Unit of Neuro-Oncoematologia, Santa Lucia Foundation IRCCS, 00143 Rome, Italy
| | - Giuseppe Zardo
- Department of Experimental Medicine, Sapienza University, 00185 Rome, Italy;
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Napoli G, Panzironi N, Traversa A, Catalanotto C, Pace V, Petrizzelli F, Giovannetti A, Lazzari S, Cogoni C, Tartaglia M, Carella M, Mazza T, Pizzuti A, Parisi C, Caputo V. Potassium Channel KCNH1 Activating Variants Cause Altered Functional and Morphological Ciliogenesis. Mol Neurobiol 2022; 59:4825-4838. [PMID: 35639255 PMCID: PMC9363390 DOI: 10.1007/s12035-022-02886-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/17/2022] [Indexed: 12/18/2022]
Abstract
The primary cilium is a non-motile sensory organelle that extends from the surface of most vertebrate cells and transduces signals regulating proliferation, differentiation, and migration. Primary cilia dysfunctions have been observed in cancer and in a group of heterogeneous disorders called ciliopathies, characterized by renal and liver cysts, skeleton and limb abnormalities, retinal degeneration, intellectual disability, ataxia, and heart disease and, recently, in autism spectrum disorder, schizophrenia, and epilepsy. The potassium voltage-gated channel subfamily H member 1 (KCNH1) gene encodes a member of the EAG (ether-à-go-go) family, which controls potassium flux regulating resting membrane potential in both excitable and non-excitable cells and is involved in intracellular signaling, cell proliferation, and tumorigenesis. KCNH1 missense variants have been associated with syndromic neurodevelopmental disorders, including Zimmermann-Laband syndrome 1 (ZLS1, MIM #135500), Temple-Baraitser syndrome (TMBTS, MIM #611816), and, recently, with milder phenotypes as epilepsy. In this work, we provide evidence that KCNH1 localizes at the base of the cilium in pre-ciliary vesicles and ciliary pocket of human dermal fibroblasts and retinal pigment epithelial (hTERT RPE1) cells and that the pathogenic missense variants (L352V and R330Q; NP_002229.1) perturb cilia morphology, assembly/disassembly, and Sonic Hedgehog signaling, disclosing a multifaceted role of the protein. The study of KCNH1 localization, its functions related to primary cilia, and the alterations introduced by mutations in ciliogenesis, cell cycle coordination, cilium morphology, and cilia signaling pathways could help elucidate the molecular mechanisms underlying neurological phenotypes and neurodevelopmental disorders not considered as classical ciliopathies but for which a significant role of primary cilia is emerging.
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Affiliation(s)
- Giulia Napoli
- Institute of Biochemistry and Cell Biology, CNR-National Research Council, Monterotondo Scalo, Rome, Italy
| | - Noemi Panzironi
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Alice Traversa
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | | | - Valentina Pace
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesco Petrizzelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Agnese Giovannetti
- Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Sara Lazzari
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Carlo Cogoni
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Massimo Carella
- Research Unit of Medical Genetics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo Della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Chiara Parisi
- Institute of Biochemistry and Cell Biology, CNR-National Research Council, Monterotondo Scalo, Rome, Italy.
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
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Martella M, Catalanotto C, Talora C, La Teana A, Londei P, Benelli D. Inhibition of Eukaryotic Translation Initiation Factor 5A (eIF5A) Hypusination Suppress p53 Translation and Alters the Association of eIF5A to the Ribosomes. Int J Mol Sci 2020; 21:E4583. [PMID: 32605139 PMCID: PMC7369855 DOI: 10.3390/ijms21134583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/17/2020] [Accepted: 06/25/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic translation initiation factor 5A (eIF5A) is an essential protein for the viability of the cells whose proposed function is to prevent the stalling of the ribosomes during translation elongation. eIF5A activity requires a unique and functionally essential post-translational modification, the change of a lysine to hypusine. eIF5A is recognized as a promoter of cell proliferation, but it has also been suggested to induce apoptosis. To date, the precise molecular mechanism through which eIF5A affects these processes remains elusive. In the present study, we explored whether eIF5A is involved in controlling the stress-induced expression of the key cellular regulator p53. Our results show that treatment of HCT-116 colon cancer cells with the deoxyhypusine (DHS) inhibitor N1-guanyl-1,7-diamineheptane (GC7) caused both inhibition of eIF5A hypusination and a significant reduction of p53 expression in UV-treated cells, and that eIF5A controls p53 expression at the level of protein synthesis. Furthermore, we show that treatment with GC7 followed by UV-induced stress counteracts the pro-apoptotic process triggered by p53 up-regulation. More in general, the importance of eIF5A in the cellular stress response is illustrated by the finding that exposure to UV light promotes the binding of eIF5A to the ribosomes, whereas UV treatment complemented by the presence of GC7 inhibits such binding, allowing a decrease of de novo synthesis of p53 protein.
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Affiliation(s)
- Marianna Martella
- Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, UK
| | - Caterina Catalanotto
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291/324, 00161 Rome, Italy; (C.C.); (C.T.); (P.L.)
| | - Claudio Talora
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291/324, 00161 Rome, Italy; (C.C.); (C.T.); (P.L.)
| | - Anna La Teana
- Department of Life and Environmental Science, Polytechnic University of Marche, 60131 Ancona, Italy;
| | - Paola Londei
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291/324, 00161 Rome, Italy; (C.C.); (C.T.); (P.L.)
| | - Dario Benelli
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291/324, 00161 Rome, Italy; (C.C.); (C.T.); (P.L.)
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Scalea S, Maresca C, Catalanotto C, Marino R, Cogoni C, Reale A, Zampieri M, Zardo G. Modifications of H3K4 methylation levels are associated with DNA hypermethylation in acute myeloid leukemia. FEBS J 2019; 287:1155-1175. [PMID: 31599112 DOI: 10.1111/febs.15086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/02/2019] [Accepted: 10/06/2019] [Indexed: 01/07/2023]
Abstract
The 'instructive model' of aberrant DNA methylation in human tumors is based on the observation that CpG islands prone to hypermethylation in cancers are embedded in chromatin enriched in H3K27me3 in human embryonic stem cells (hESC). Recent studies also link methylation of CpG islands to the methylation status of H3K4, where H3K4me3 is inversely correlated with DNA methylation. To provide insight into these conflicting findings, we generated DNA methylation profiles for acute myeloid leukemia samples from patients and leukemic cell lines and integrated them with publicly available ChIp-seq data, containing H3K4me3 and H3K27me3 CpG island occupation in hESC, or hematopoietic stem or progenitor cells (hHSC/MPP). Hypermethylated CpG islands in AML samples displayed H3K27me3 enrichments in hESC and hHSC/MPP; however, ChIp analysis of specific hypermethylated CpG islands revealed a significant reduction in H3K4me3 signal with a concomitant increase in H3K4me0 levels as opposed to a nonsignificant increase in H3K27me3 marks. The integration of AML DNA methylation profiles with the ChIp-seq data in hESC and hHSC/MPP also led to the identification of Iroquois homeobox 2 (IRX2) as a previously unknown factor promoting differentiation of leukemic cells. Our results indicate that in contrast to the 'instructive model', H3K4me3 levels are strongly associated with DNA methylation patterns in AML and have a role in the regulation of critical genes, such as the putative tumor suppressor IRX2.
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Affiliation(s)
- Stefania Scalea
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
| | - Carmen Maresca
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome, Italy
| | | | - Rachele Marino
- Department of Molecular Medicine, University of Rome, Sapienza, Italy
| | - Carlo Cogoni
- Department of Molecular Medicine, University of Rome, Sapienza, Italy
| | - Anna Reale
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
| | - Michele Zampieri
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
| | - Giuseppe Zardo
- Department of Experimental Medicine, University of Rome, Sapienza, Italy
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Paolantoni C, Ricciardi S, De Paolis V, Okenwa C, Catalanotto C, Ciotti MT, Cattaneo A, Cogoni C, Giorgi C. Arc 3' UTR Splicing Leads to Dual and Antagonistic Effects in Fine-Tuning Arc Expression Upon BDNF Signaling. Front Mol Neurosci 2018; 11:145. [PMID: 29755318 PMCID: PMC5934489 DOI: 10.3389/fnmol.2018.00145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/10/2018] [Indexed: 01/02/2023] Open
Abstract
Activity-regulated cytoskeletal associated protein (Arc) is an immediate-early gene critically involved in synaptic plasticity and memory consolidation. Arc mRNA is rapidly induced by synaptic activation and a portion is locally translated in dendrites where it modulates synaptic strength. Being an activity-dependent effector of homeostatic balance, regulation of Arc is uniquely tuned to result in short-lived bursts of expression. Cis-Acting elements that control its transitory expression post-transcriptionally reside primarily in Arc mRNA 3′ UTR. These include two conserved introns which distinctively modulate Arc mRNA stability by targeting it for destruction via the nonsense mediated decay pathway. Here, we further investigated how splicing of the Arc mRNA 3′ UTR region contributes to modulate Arc expression in cultured neurons. Unexpectedly, upon induction with brain derived neurotrophic factor, translational efficiency of a luciferase reporter construct harboring Arc 3′ UTR is significantly upregulated and this effect is dependent on splicing of Arc introns. We find that, eIF2α dephosphorylation, mTOR, ERK, PKC, and PKA activity are key to this process. Additionally, CREB-dependent transcription is required to couple Arc 3′ UTR-splicing to its translational upregulation, suggesting the involvement of de novo transcribed trans-acting factors. Overall, splicing of Arc 3′ UTR exerts a dual and unique effect in fine-tuning Arc expression upon synaptic signaling: while inducing mRNA decay to limit the time window of Arc expression, it also elicits translation of the decaying mRNA. This antagonistic effect likely contributes to the achievement of a confined yet efficient burst of Arc protein expression, facilitating its role as an effector of synapse-specific plasticity.
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Affiliation(s)
- Chiara Paolantoni
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy.,Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Simona Ricciardi
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy.,Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Veronica De Paolis
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy.,Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Chinenye Okenwa
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy
| | - Caterina Catalanotto
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
| | - Maria T Ciotti
- Institute of Cell Biology and Neurobiology, National Research Council, Rome, Italy
| | - Antonino Cattaneo
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy.,Bio@SNS Laboratory, Scuola Normale Superiore, Pisa, Italy
| | - Carlo Cogoni
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
| | - Corinna Giorgi
- European Brain Research Institute Rita Levi-Montalcini Rome, Rome, Italy
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Catalanotto C, Cogoni C, Zardo G. MicroRNA in Control of Gene Expression: An Overview of Nuclear Functions. Int J Mol Sci 2016; 17:ijms17101712. [PMID: 27754357 PMCID: PMC5085744 DOI: 10.3390/ijms17101712] [Citation(s) in RCA: 736] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/04/2016] [Accepted: 10/07/2016] [Indexed: 12/14/2022] Open
Abstract
The finding that small non-coding RNAs (ncRNAs) are able to control gene expression in a sequence specific manner has had a massive impact on biology. Recent improvements in high throughput sequencing and computational prediction methods have allowed the discovery and classification of several types of ncRNAs. Based on their precursor structures, biogenesis pathways and modes of action, ncRNAs are classified as small interfering RNAs (siRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs), promoter associate RNAs (pRNAs), small nucleolar RNAs (snoRNAs) and sno-derived RNAs. Among these, miRNAs appear as important cytoplasmic regulators of gene expression. miRNAs act as post-transcriptional regulators of their messenger RNA (mRNA) targets via mRNA degradation and/or translational repression. However, it is becoming evident that miRNAs also have specific nuclear functions. Among these, the most studied and debated activity is the miRNA-guided transcriptional control of gene expression. Although available data detail quite precisely the effectors of this activity, the mechanisms by which miRNAs identify their gene targets to control transcription are still a matter of debate. Here, we focus on nuclear functions of miRNAs and on alternative mechanisms of target recognition, at the promoter lavel, by miRNAs in carrying out transcriptional gene silencing.
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Affiliation(s)
- Caterina Catalanotto
- Department of Cellular Biotechnologies and Hematology, University of Rome Sapienza, Rome 00179, Italy.
| | - Carlo Cogoni
- Department of Cellular Biotechnologies and Hematology, University of Rome Sapienza, Rome 00179, Italy.
| | - Giuseppe Zardo
- Department of Cellular Biotechnologies and Hematology, University of Rome Sapienza, Rome 00179, Italy.
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Pilozzi E, Maresca C, Duranti E, Giustiniani MC, Catalanotto C, Lucarelli M, Cogoni C, Ferri M, Ruco L, Zardo G. Left-sided early-onset vs late-onset colorectal carcinoma: histologic, clinical, and molecular differences. Am J Clin Pathol 2015; 143:374-84. [PMID: 25696795 DOI: 10.1309/ajcpnoc55iolxfud] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Carcinomas of the left colon represent a neoplasm of older patients (late onset), but epidemiologic evidence has been showing an increasing incidence in patients 50 years or younger (early onset). In this study, we investigate pathologic and molecular features of early- and late-onset carcinoma of the left colon. METHODS We selected 22 patients 50 years or younger and 21 patients 70 years or older with left-sided colorectal carcinoma (CRC). All samples were evaluated for pathologic features, microsatellite instability, and KRAS and BRAF mutations. Moreover, both groups were analyzed to identify CpG island methylator phenotype features and assessed with restriction landmark genome scanning (RLGS) to unveil differential DNA methylation patterns. RESULTS Early-onset patients had advanced pathologic stages compared with late-onset patients (P = .0482). All cases showed a microsatellite stable profile and BRAF wild-type sequence. Early-onset patients (43%) more frequently had mutations at KRAS codon 12 compared with late-onset patients (14%) (P =.0413). RLGS showed that patients younger than 50 years who had CRC had a significantly lower percentage of methylated loci than did patients 70 years or older (P = .04124), and differential methylation of several genomic loci was observed in the two groups. CONCLUSIONS Our results suggest that left-sided CRCs may present differential patterns of aberrant DNA methylation when they are separated by age.
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Affiliation(s)
- Emanuela Pilozzi
- Department of Clinical and Molecular Medicine, Sant’Andrea Hospital, University of Rome “La Sapienza,” Rome, Italy
| | - Carmen Maresca
- Department of Cellular Biotechnologies and Hematology, University of Rome “La Sapienza”, Rome, Italy
| | - Enrico Duranti
- Department of Clinical and Molecular Medicine, Sant’Andrea Hospital, University of Rome “La Sapienza,” Rome, Italy
| | | | - Caterina Catalanotto
- Department of Cellular Biotechnologies and Hematology, University of Rome “La Sapienza”, Rome, Italy
| | - Marco Lucarelli
- Department of Cellular Biotechnologies and Hematology, University of Rome “La Sapienza”, Rome, Italy
| | - Carlo Cogoni
- Department of Cellular Biotechnologies and Hematology, University of Rome “La Sapienza”, Rome, Italy
| | - Mario Ferri
- Department of Medical-Surgical Sciences and Translation Medicine, Sant’Andrea Hospital, University of Rome “La Sapienza,” Rome, Italy
| | - Luigi Ruco
- Department of Clinical and Molecular Medicine, Sant’Andrea Hospital, University of Rome “La Sapienza,” Rome, Italy
| | - Giuseppe Zardo
- Department of Cellular Biotechnologies and Hematology, University of Rome “La Sapienza”, Rome, Italy
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9
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Giorgi C, Cogoni C, Catalanotto C. From transcription to translation: new insights in the structure and function of Argonaute protein. Biomol Concepts 2014; 3:545-59. [PMID: 25436558 DOI: 10.1515/bmc-2012-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 07/20/2012] [Indexed: 11/15/2022] Open
Abstract
Abstract Argonaute proteins play a central role in gene silencing pathways mediated by small RNA molecules. The ancestral function of small RNA-dependent silencing is related to genome protection against parasitic nucleic acids, such as transposons and viruses. However, new classes of small RNAs are continuously being uncovered in all higher eukaryotes in which they play important functions in processes ranging from embryonic development to differentiation to cell proliferation and metabolism. Small RNAs have variegated biogenesis pathways and accomplish distinct functions. Nevertheless, it appears that all small RNAs work merely as guides in recognizing the target RNAs invariably relying on the interaction with Argonaute proteins and associated factors for their biological function. Here, we discuss recent findings on the structure and regulation of mammalian Argonaute proteins and overview the various roles that these versatile proteins play in regulating gene expression.
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Caputo V, Sinibaldi L, Fiorentino A, Parisi C, Catalanotto C, Pasini A, Cogoni C, Pizzuti A. Brain derived neurotrophic factor (BDNF) expression is regulated by microRNAs miR-26a and miR-26b allele-specific binding. PLoS One 2011; 6:e28656. [PMID: 22194877 PMCID: PMC3237476 DOI: 10.1371/journal.pone.0028656] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 11/12/2011] [Indexed: 01/08/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is a neurotrophin that plays an essential role in neuronal development and plasticity. MicroRNA (miRNAs) are small non-coding RNAs of about 22-nucleotides in length regulating gene expression at post-transcriptional level. In this study we explore the role of miRNAs as post-transcriptional inhibitors of BDNF and the effect of 3′UTR sequence variations on miRNAs binding capacity. Using an in silico approach we identified a group of miRNAs putatively regulating BDNF expression and binding to BDNF 3′UTR polymorphic sequences. Luciferase assays demonstrated that these miRNAs (miR-26a1/2 and miR-26b) downregulates BDNF expression and that the presence of the variant alleles of two single nucleotide polymorphisms (rs11030100 and rs11030099) mapping in BDNF 3′UTR specifically abrogates miRNAs targeting. Furthermore we found a high linkage disequilibrium rate between rs11030100, rs11030099 and the non-synonymous coding variant rs6265 (Val66Met), which modulates BDNF mRNA localization and protein intracellular trafficking. Such observation led to hypothesize that miR-26s mediated regulation could extend to rs6265 leading to an allelic imbalance with potentially functional effects, such as peptide's localization and activity-dependent secretion. Since rs6265 has been previously implicated in various neuropsychiatric disorders, we evaluated the distribution of rs11030100, rs11030099 and rs6265 both in a control and schizophrenic group, but no significant difference in allele frequencies emerged. In conclusion, in the present study we identified two novel miRNAs regulating BDNF expression and the first BDNF 3′UTR functional variants altering miRNAs-BDNF binding.
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Affiliation(s)
- Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
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Parisi C, Giorgi C, Batassa EM, Braccini L, Maresca G, D'agnano I, Caputo V, Salvatore A, Pietrolati F, Cogoni C, Catalanotto C. Ago1 and Ago2 differentially affect cell proliferation, motility and apoptosis when overexpressed in SH-SY5Y neuroblastoma cells. FEBS Lett 2011; 585:2965-71. [PMID: 21846468 DOI: 10.1016/j.febslet.2011.08.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/01/2011] [Accepted: 08/01/2011] [Indexed: 01/20/2023]
Abstract
Argonaute are a conserved class of proteins central to the microRNA pathway. We have highlighted a novel and non-redundant function of Ago1 versus Ago2; the two core factors of the miRNA-associated RISC complex. Stable overexpression of Ago1 in neuroblastoma cells causes the cell cycle to slow down, a decrease in cellular motility and a stronger apoptotic response upon UV irradiation. These effects, together with a significant increase in p53 levels, suggest that Ago1 may act as a tumor-suppressor factor, a function also supported by GEO Profiles microarrays that inversely correlate Ago1 expression levels with cell proliferation rates.
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Affiliation(s)
- Chiara Parisi
- Department of Cellular Biotechnology and Hematology, Sapienza University, Rome, Italy
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Abstract
MicroRNAs (miRNAs) are a recently discovered class of small RNA molecules implicated in a wide range of diverse gene regulatory mechanisms. Interestingly, numerous miRNAs are expressed in a spatially and temporally controlled manner in the nervous system. This suggests that gene regulation networks based on miRNA activities may be particularly relevant in neurons. Recent studies show the involvement of RNA-mediated gene silencing in neurogenesis, neural differentiation, synaptic plasticity, and neurologic and psychiatric diseases. This review focuses on the roles of miRNAs in the gene regulation of the nervous system.
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Affiliation(s)
- Christian Barbato
- European Brain Research Institute (EBRI), Fondazione EBRI, Rita Levi-Montalcini Via del Fosso di Fiorano, 64/65, 00143 Roma, Italy.
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Nolan T, Cecere G, Mancone C, Alonzi T, Tripodi M, Catalanotto C, Cogoni C. The RNA-dependent RNA polymerase essential for post-transcriptional gene silencing in Neurospora crassa interacts with replication protein A. Nucleic Acids Res 2007; 36:532-8. [PMID: 18048414 PMCID: PMC2241871 DOI: 10.1093/nar/gkm1071] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Post-transcriptional gene silencing (PTGS) pathways play a role in genome defence and have been extensively studied, yet how repetitive elements in the genome are identified is still unclear. It has been suggested that they may produce aberrant transcripts (aRNA) that are converted by an RNA-dependent RNA polymerase (RdRP) into double-stranded RNA (dsRNA), the essential intermediate of PTGS. However, how RdRP enzymes recognize aberrant transcripts remains a key question. Here we show that in Neurospora crassa the RdRP QDE-1 interacts with Replication Protein A (RPA), part of the DNA replication machinery. We show that both QDE-1 and RPA are nuclear proteins and that QDE-1 is specifically recruited onto the repetitive transgenic loci. We speculate that this localization of QDE-1 could allow the in situ production of dsRNA using transgenic nascent transcripts as templates, as in other systems. Supporting a link between the two proteins, we found that the accumulation of short interfering RNAs (siRNAs), the hallmark of silencing, is dependent on an ongoing DNA synthesis. The interaction between QDE-1 and RPA is important since it should guide further studies aimed at understanding the specificity of the RdRP and it provides for the first time a potential link between a PTGS component and the DNA replication machinery.
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Affiliation(s)
- Tony Nolan
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Università La Sapienza, Rome, Italy
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Abstract
It has become clear in the past few years that eukaryotic organisms possess different genetic systems to counter viruses, transposons and other repeated elements such as transgenes that could otherwise accumulate in the genome. In addition to serving as a model organism for genetic, biochemical and molecular studies, Neurospora crassa has proved to be a paradigm for the study of gene-silencing mechanisms. Indeed, its genome can be protected from expansion of selfish nucleic acids by a variety of mechanisms that inactivate duplicated sequences. Studies of these mechanisms have made a fundamental contribution to the understanding of the gene-silencing field.
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Affiliation(s)
- Caterina Catalanotto
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Policlinico Umberto I, Universita' degli Studi di Roma 'La Sapienza', Roma, Italy
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Catalanotto C, Pallotta M, ReFalo P, Sachs MS, Vayssie L, Macino G, Cogoni C. Redundancy of the two dicer genes in transgene-induced posttranscriptional gene silencing in Neurospora crassa. Mol Cell Biol 2004; 24:2536-45. [PMID: 14993290 PMCID: PMC355837 DOI: 10.1128/mcb.24.6.2536-2545.2004] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA interference (RNAi) in animals, cosuppression in plants, and quelling in fungi are homology-dependent gene silencing mechanisms in which the introduction of either double-stranded RNA (dsRNA) or transgenes induces sequence-specific mRNA degradation. These phenomena share a common genetic and mechanistic basis. The accumulation of short interfering RNA (siRNA) molecules that guide sequence-specific mRNA degradation is a common feature in both silencing mechanisms, as is the component of the RNase complex involved in mRNA cleavage. During RNAi in animal cells, dsRNA is processed into siRNA by an RNase III enzyme called Dicer. Here we show that elimination of the activity of two Dicer-like genes by mutation in the fungus Neurospora crassa eliminates transgene-induced gene silencing (quelling) and the processing of dsRNA to an siRNA form. The two Dicer-like genes appear redundant because single mutants are quelling proficient. This first demonstration of the involvement of Dicer in gene silencing induced by transgenes supports a model by which a dsRNA produced by the activity of cellular RNA-dependent RNA polymerases on transgenic transcripts is an essential intermediate of silencing.
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Affiliation(s)
- Caterina Catalanotto
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Universita' di Roma La Sapienza, 00161 Rome, Italy
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Affiliation(s)
- Annette S Pickford
- Department of Cellular and Hematologic Biotechnology, Università di Roma La Sapienza, Rome, Italy
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Abstract
Small RNA molecules have been found to be specifically associated with posttranscriptional gene silencing (PTGS) in both plants and animals. Here, we find that small sense and antisense RNAs are also involved in PTGS in Neurospora crassa. The accumulation of these RNA molecules depends on the presence of functional qde-1 and qde-3 genes previously shown to be essential for gene silencing, but does not depend on a functional qde-2, indicating that this gene is involved in a downstream step of the gene silencing pathway. Supporting this idea, a purified QDE2 protein complex was found to contain small RNA molecules, suggesting that QDE2 could be part of a small RNA-directed ribonuclease complex involved in sequence-specific mRNA degradation.
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Affiliation(s)
- Caterina Catalanotto
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università di Roma La Sapienza, 00161 Roma, Italy
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18
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Affiliation(s)
- C Catalanotto
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Universita' di Roma La Sapienza, Italy
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