1
|
Liu Y, Wai AP, Zolzaya T, Iida Y, Okada S, Iizasa H, Yoshiyama H. Exploring the anti-EBV potential of suberoylanilide hydroxamic acid: Induction of apoptosis in infected cells through suppressing BART gene expression and inducing lytic infection. Virology 2024; 597:110161. [PMID: 38981317 DOI: 10.1016/j.virol.2024.110161] [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: 03/29/2024] [Revised: 06/09/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
Epstein-Barr virus (EBV) is linked to lymphoma and epithelioma but lacks drugs specifically targeting EBV-positive tumors. BamHI A Rightward Transcript (BART) miRNAs are expressed in all EBV-positive tumors, suppressing both lytic infection and host cell apoptosis. We identified suberoylanilide hydroxamic acid (SAHA), an inhibitor of histone deacetylase enzymes, as an agent that suppresses BART promoter activity and transcription of BART miRNAs. SAHA treatment demonstrated a more pronounced inhibition of cell proliferation in EBV-positive cells compared to EBV-negative cells, affecting both p53 wild-type and mutant gastric epithelial cells. SAHA treatment enhanced lytic infection in wild-type EBV-infected cells, while also enhancing cell death in BZLF1-deficient EBV-infected cells. It reduced BART gene expression by 85% and increased the expression of proapoptotic factors targeted by BART miRNAs. These findings suggest that SAHA not only induces lytic infection but also leads to cell death by suppressing BART miRNA transcription and promoting the apoptotic program.
Collapse
Affiliation(s)
- Yuxin Liu
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Aung Phyo Wai
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Tumurgan Zolzaya
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Yuichi Iida
- Department of Immunology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Shunpei Okada
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Hisashi Iizasa
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Hironori Yoshiyama
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| |
Collapse
|
2
|
Murphy MR, Ramadei A, Doymaz A, Varriano S, Natelson D, Yu A, Aktas S, Mazzeo M, Mazzeo M, Zakusilo G, Kleiman F. Long non-coding RNA generated from CDKN1A gene by alternative polyadenylation regulates p21 expression during DNA damage response. Nucleic Acids Res 2023; 51:11911-11926. [PMID: 37870464 PMCID: PMC10681730 DOI: 10.1093/nar/gkad899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 09/21/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
Alternative Polyadenylation (APA) is an emerging mechanism for dynamic changes in gene expression. Previously, we described widespread APA occurrence in introns during the DNA damage response (DDR). Here, we show that a DDR-activated APA event occurs in the first intron of CDKN1A, inducing an alternate last exon-containing lncRNA. We named this lncRNA SPUD (Selective Polyadenylation Upon DNA Damage). SPUD localizes to polysomes in the cytoplasm and is detectable as multiple isoforms in available high-throughput studies. SPUD has low abundance compared to the CDKN1A full-length isoform under non-stress conditions, and SPUD is induced in cancer and normal cells under a variety of DNA damaging conditions in part through p53. The RNA binding protein HuR binds to and promotes the stability of SPUD precursor RNA. SPUD induction increases p21 protein, but not mRNA levels, affecting p21 functions in cell-cycle, CDK2 expression and cell growth. Like CDKN1A full-length isoform, SPUD can bind two competitive p21 translational regulators, the inhibitor calreticulin and the activator CUGBP1; SPUD alters their association with CDKN1A full-length in a DDR-dependent manner, promoting CDKN1A translation. Together, these results show a new regulatory mechanism by which a lncRNA controls p21 expression post-transcriptionally, highlighting lncRNA relevance in DDR progression and cell-cycle.
Collapse
Affiliation(s)
- Michael R Murphy
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Anthony Ramadei
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Ahmet Doymaz
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Sophia Varriano
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Devorah M Natelson
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Amy Yu
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Sera Aktas
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Marie Mazzeo
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Michael Mazzeo
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - George Zakusilo
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Frida E Kleiman
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| |
Collapse
|
3
|
Yin J, Seo Y, Rhim J, Jin X, Kim TH, Kim SS, Hong JH, Gwak HS, Yoo H, Park JB, Kim JH. Cross-talk between PARN and EGFR-STAT3 Signaling Facilitates Self-Renewal and Proliferation of Glioblastoma Stem Cells. Cancer Res 2023; 83:3693-3709. [PMID: 37747775 DOI: 10.1158/0008-5472.can-22-3965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/19/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
Glioblastoma is the most common type of malignant primary brain tumor and displays highly aggressive and heterogeneous phenotypes. The transcription factor STAT3 has been reported to play a key role in glioblastoma malignancy. Thus, discovering targets and functional downstream networks regulated by STAT3 that govern glioblastoma pathogenesis may lead to improved treatment strategies. In this study, we identified that poly(A)-specific ribonuclease (PARN), a key modulator of RNA metabolism, activates EGFR-STAT3 signaling to support glioblastoma stem cells (GSC). Functional integrative analysis of STAT3 found PARN as the top-scoring transcriptional target involved in RNA processing in patients with glioblastoma, and PARN expression was strongly correlated with poor patient survival and elevated malignancy. PARN positively regulated self-renewal and proliferation of GSCs through its 3'-5' exoribonuclease activity. EGFR was identified as a clinically relevant target of PARN in GSCs. PARN positively modulated EGFR by negatively regulating the EGFR-targeting miRNA miR-7, and increased EGFR expression created a positive feedback loop to increase STAT3 activation. PARN depletion in GSCs reduced infiltration and prolonged survival in orthotopic brain tumor xenografts; similar results were observed using siRNA nanocapsule-mediated PARN targeting. Pharmacological targeting of STAT3 also confirmed PARN regulation by STAT3 signaling. In sum, these results suggest that a STAT3-PARN regulatory network plays a pivotal role in tumor progression and thus may represent a target for glioblastoma therapeutics. SIGNIFICANCE A positive feedback loop comprising PARN and EGFR-STAT3 signaling supports self-renewal and proliferation of glioblastoma stem cells to drive tumor progression and can be targeted in glioblastoma therapeutics.
Collapse
Affiliation(s)
- Jinlong Yin
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Yoona Seo
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Jiho Rhim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Xiong Jin
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Tae Hoon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Sung Soo Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Jun-Hee Hong
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Ho-Shin Gwak
- Neuro-Oncology Clinic, National Cancer Center, Goyang, Korea
- Department of Cancer Control, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Heon Yoo
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Neuro-Oncology Clinic, National Cancer Center, Goyang, Korea
| | - Jong Bae Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Jong Heon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
| |
Collapse
|
4
|
Huynh TN, Parker R. The PARN, TOE1, and USB1 RNA deadenylases and their roles in non-coding RNA regulation. J Biol Chem 2023; 299:105139. [PMID: 37544646 PMCID: PMC10493513 DOI: 10.1016/j.jbc.2023.105139] [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: 05/13/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023] Open
Abstract
The levels of non-coding RNAs (ncRNAs) are regulated by transcription, RNA processing, and RNA degradation pathways. One mechanism for the degradation of ncRNAs involves the addition of oligo(A) tails by non-canonical poly(A) polymerases, which then recruit processive sequence-independent 3' to 5' exonucleases for RNA degradation. This pathway of decay is also regulated by three 3' to 5' exoribonucleases, USB1, PARN, and TOE1, which remove oligo(A) tails and thereby can protect ncRNAs from decay in a manner analogous to the deubiquitination of proteins. Loss-of-function mutations in these genes lead to premature degradation of some ncRNAs and lead to specific human diseases such as Poikiloderma with Neutropenia (PN) for USB1, Dyskeratosis Congenita (DC) for PARN and Pontocerebellar Hypoplasia type 7 (PCH7) for TOE1. Herein, we review the biochemical properties of USB1, PARN, and TOE1, how they modulate ncRNA levels, and their roles in human diseases.
Collapse
Affiliation(s)
- Thao Ngoc Huynh
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
| |
Collapse
|
5
|
Murphy MR, Ramadei A, Doymaz A, Varriano S, Natelson D, Yu A, Aktas S, Mazzeo M, Mazzeo M, Zakusilo G, Kleiman FE. Long Non-Coding RNA Generated from CDKN1A Gene by Alternative Polyadenylation Regulates p21 Expression during DNA Damage Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523318. [PMID: 36711808 PMCID: PMC9882041 DOI: 10.1101/2023.01.10.523318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Alternative Polyadenylation (APA) is an emerging mechanism for dynamic changes in gene expression. Previously, we described widespread APA occurrence in introns during the DNA damage response (DDR). Here, we show that a DNA damage activated APA event occurs in the first intron of CDKN1A , inducing an alternate last exon (ALE)-containing lncRNA. We named this lncRNA SPUD (Selective Polyadenylation Upon Damage). SPUD localizes to polysomes in the cytoplasm and is detectable as multiple isoforms in available high throughput studies. SPUD has low abundance compared to the CDKN1A full-length isoform and is induced in cancer and normal cells under a variety of DNA damaging conditions in part through p53 transcriptional activation. RNA binding protein (RBP) HuR and the transcriptional repressor CTCF regulate SPUD levels. SPUD induction increases p21 protein, but not CDKN1A full-length levels, affecting p21 functions in cell-cycle, CDK2 expression, and cell viability. Like CDKN1A full-length isoform, SPUD can bind two competitive p21 translational regulators, the inhibitor calreticulin and the activator CUGBP1; SPUD can change their association with CDKN1A full-length in a DDR-dependent manner. Together, these results show a new regulatory mechanism by which a lncRNA controls p21 expression post-transcriptionally, highlighting lncRNA relevance in DDR progression and cellcycle.
Collapse
|
6
|
EpisomiR, a New Family of miRNAs, and Its Possible Roles in Human Diseases. Biomedicines 2022; 10:biomedicines10061280. [PMID: 35740302 PMCID: PMC9220071 DOI: 10.3390/biomedicines10061280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 11/26/2022] Open
Abstract
MicroRNAs (miRNAs) are synthesized through a canonical pathway and play a role in human diseases, such as cancers and cardiovascular, neurodegenerative, psychiatric, and chronic inflammatory diseases. The development of sequencing technologies has enabled the identification of variations in noncoding miRNAs. These miRNA variants, called isomiRs, are generated through a non-canonical pathway, by several enzymes that alter the length and sequence of miRNAs. The isomiR family is, now, expanding further to include episomiRs, which are miRNAs with different modifications. Since recent findings have shown that isomiRs reflect the cell-specific biological function of miRNAs, knowledge about episomiRs and isomiRs can, possibly, contribute to the optimization of diagnosis and therapeutic technology for precision medicine.
Collapse
|
7
|
Kyritsis A, Papanastasi E, Kokkori I, Maragozidis P, Chatzileontiadou DSM, Pallaki P, Labrou M, Zarogiannis SG, Chrousos GP, Vlachakis D, Gourgoulianis KI, Balatsos NAA. Integrated Deadenylase Genetic Association Network and Transcriptome Analysis in Thoracic Carcinomas. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103102. [PMID: 35630580 PMCID: PMC9145511 DOI: 10.3390/molecules27103102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 12/03/2022]
Abstract
The poly(A) tail at the 3′ end of mRNAs determines their stability, translational efficiency, and fate. The shortening of the poly(A) tail, and its efficient removal, triggers the degradation of mRNAs, thus, regulating gene expression. The process is catalyzed by a family of enzymes, known as deadenylases. As the dysregulation of gene expression is a hallmark of cancer, understanding the role of deadenylases has gained additional interest. Herein, the genetic association network shows that CNOT6 and CNOT7 are the most prevalent and most interconnected nodes in the equilibrated diagram. Subsequent silencing and transcriptomic analysis identifies transcripts possibly regulated by specific deadenylases. Furthermore, several gene ontologies are enriched by common deregulated genes. Given the potential concerted action and overlapping functions of deadenylases, we examined the effect of silencing a deadenylase on the remaining ones. Our results suggest that specific deadenylases target unique subsets of mRNAs, whilst at the same time, multiple deadenylases may affect the same mRNAs with overlapping functions.
Collapse
Affiliation(s)
- Athanasios Kyritsis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
| | - Eirini Papanastasi
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Ioanna Kokkori
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
- Department of Pneumonology-Oncology, Theagenio Cancer Hospital, 540 07 Thessaloniki, Greece
| | - Panagiotis Maragozidis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Demetra S. M. Chatzileontiadou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Paschalina Pallaki
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Maria Labrou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
| | - Sotirios G. Zarogiannis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
- Department of Physiology, Faculty of Medicine, University of Thessaly, Biopolis, 415 00 Larissa, Greece
- Correspondence: (S.G.Z.); (K.I.G.); (N.A.A.B.)
| | - George P. Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (G.P.C.); (D.V.)
- UNESCO Chair on Adolescent Health Care, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Center of Clinical, Experimental Surgery and Translational Research, Division of Endocrinology and Metabolism, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
| | - Dimitrios Vlachakis
- University Research Institute of Maternal and Child Health and Precision Medicine, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece; (G.P.C.); (D.V.)
- UNESCO Chair on Adolescent Health Care, ‘Aghia Sophia’ Children’s Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Center of Clinical, Experimental Surgery and Translational Research, Division of Endocrinology and Metabolism, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 118 55 Athens, Greece
| | - Konstantinos I. Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, 411 10 Larissa, Greece;
- Correspondence: (S.G.Z.); (K.I.G.); (N.A.A.B.)
| | - Nikolaos A. A. Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 415 00 Larissa, Greece; (A.K.); (E.P.); (P.M.); (D.S.M.C.); (P.P.); (M.L.)
- Correspondence: (S.G.Z.); (K.I.G.); (N.A.A.B.)
| |
Collapse
|
8
|
Nanjappa DP, Babu N, Khanna-Gupta A, O'Donohue MF, Sips P, Chakraborty A. Poly (A)-specific ribonuclease (PARN): More than just "mRNA stock clearing". Life Sci 2021; 285:119953. [PMID: 34520768 DOI: 10.1016/j.lfs.2021.119953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, the balance between the synthesis and the degradation decides the steady-state levels of messenger RNAs (mRNA). The removal of adenosine residues from the poly(A) tail, called deadenylation, is the first and the most crucial step in the process of mRNA degradation. Poly (A)-specific ribonuclease (PARN) is one such enzyme that catalyses the process of deadenylation. Although PARN has been primarily known as the regulator of the mRNA stability, recent evidence clearly suggests several other functions of PARN, including a role in embryogenesis, oocyte maturation, cell-cycle progression, telomere biology, non-coding RNA maturation and ribosome biogenesis. Also, deregulated PARN activity is shown to be a hallmark of specific disease conditions. Pathogenic variants in the PARN gene have been observed in various cancers and inherited bone marrow failure syndromes. The focus in this review is to highlight the emerging functions of PARN, particularly in the context of human diseases.
Collapse
Affiliation(s)
- Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakate, Mangaluru 575018, India
| | - Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakate, Mangaluru 575018, India
| | - Arati Khanna-Gupta
- Consortium of Rare Genetic and Bone Marrow Disorders, India network@NitteDU, NITTE (Deemed to be University, Deralakatte, Mangaluru, India
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative CBI, Université de Toulouse- CNRS- UPS- Toulouse-, Dynamics and Disorders of Ribosome Synthesis, Toulouse, France
| | - Patrick Sips
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakate, Mangaluru 575018, India.
| |
Collapse
|
9
|
Song XH, Liao XY, Zheng XY, Liu JQ, Zhang ZW, Zhang LN, Yan YB. Human Ccr4 and Caf1 Deadenylases Regulate Proliferation and Tumorigenicity of Human Gastric Cancer Cells via Modulating Cell Cycle Progression. Cancers (Basel) 2021; 13:cancers13040834. [PMID: 33671234 PMCID: PMC7922635 DOI: 10.3390/cancers13040834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/06/2021] [Accepted: 02/14/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Cancer cells generally reprogram their gene expression profiles to satisfy continuous growth, proliferation, and metastasis. Most eukaryotic mRNAs are degraded in a deadenylation-dependent pathway, in which deadenylases are the key enzymes. We found that human Ccr4 (hCcr4a/b) and Caf1 (hCaf1a/b), the dominant cytosolic deadenylases, were dysregulated in several types of cancers including stomach adenocarcinoma. Stably knocking down hCaf1a/b or hCcr4a/b blocks cell cycle progression by enhancing the levels of cell cycle inhibitors and by inhibiting the formation of processing bodies, which are cytosolic foci involved in mRNA metabolism. More importantly, depletion of hCaf1a/b or hCcr4a/b dramatically inhibits cell proliferation and tumorigenicity. Our results suggest that perturbating global RNA metabolism may provide a potential novel strategy for cancer treatment. Abstract Cancer cells generally have reprogrammed gene expression profiles to meet the requirements of survival, continuous division, and metastasis. An interesting question is whether the cancer cells will be affected by interfering their global RNA metabolism. In this research, we found that human Ccr4a/b (hCcr4a/b) and Caf1a/b (hCaf1a/b) deadenylases, the catalytic components of the Ccr4-Not complex, were dysregulated in several types of cancers including stomach adenocarcinoma. The impacts of the four deadenylases on cancer cell growth were studied by the establishment of four stable MKN28 cell lines with the knockdown of hCcr4a/b or hCaf1a/b or transient knockdown in several cell lines. Depletion of hCcr4a/b or hCaf1a/b significantly inhibited cell proliferation and tumorigenicity. Mechanistic studies indicated that the cells were arrested at the G2/M phase by knocking down hCaf1a, while arrested at the G0/G1 phase by depleting hCaf1b or hCcr4a/b. The four enzymes did not affect the levels of CDKs and cyclins but modulated the levels of CDK–cyclin inhibitors. We identified that hCcr4a/b, but not hCaf1a/b, targeted the p21 mRNA in the MKN28 cells. Furthermore, depletion of any one of the four deadenylases dramatically impaired processing-body formation in the MKN28 and HEK-293T cells. Our results highlight that perturbating global RNA metabolism may severely affect cancer cell proliferation, which provides a potential novel strategy for cancer treatment.
Collapse
Affiliation(s)
- Xiao-Hui Song
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Xiao-Yan Liao
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Xu-Ying Zheng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Jia-Qian Liu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Zhe-Wei Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
| | - Li-Na Zhang
- College of Life Science and Chemistry, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
- Correspondence: (L.-N.Z.); (Y.-B.Y.); Tel.: +86-10-6739-6342 (L.-N.Z.); +86-10-6278-3477 (Y.-B.Y.)
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.-H.S.); (X.-Y.L.); (X.-Y.Z.); (J.-Q.L.); (Z.-W.Z.)
- Correspondence: (L.-N.Z.); (Y.-B.Y.); Tel.: +86-10-6739-6342 (L.-N.Z.); +86-10-6278-3477 (Y.-B.Y.)
| |
Collapse
|
10
|
Yan YB. Diverse functions of deadenylases in DNA damage response and genomic integrity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1621. [PMID: 32790161 DOI: 10.1002/wrna.1621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022]
Abstract
DNA damage response (DDR) is a coordinated network of diverse cellular processes including the detection, signaling, and repair of DNA lesions, the adjustment of metabolic network and cell fate determination. To deal with the unavoidable DNA damage caused by either endogenous or exogenous stresses, the cells need to reshape the gene expression profile to allow efficient transcription and translation of DDR-responsive messenger RNAs (mRNAs) and to repress the nonessential mRNAs. A predominant method to adjust RNA fate is achieved by modulating the 3'-end oligo(A) or poly(A) length via the opposing actions of polyadenylation and deadenylation. Poly(A)-specific ribonuclease (PARN) and the carbon catabolite repressor 4 (CCR4)-Not complex, the major executors of deadenylation, are indispensable to DDR and genomic integrity in eukaryotic cells. PARN modulates cell cycle progression by regulating the stabilities of mRNAs and microRNA (miRNAs) involved in the p53 pathway and contributes to genomic stability by affecting the biogenesis of noncoding RNAs including miRNAs and telomeric RNA. The CCR4-Not complex is involved in diverse pathways of DDR including transcriptional regulation, signaling pathways, mRNA stabilities, translation regulation, and protein degradation. The RNA targets of deadenylases are tuned by the DDR signaling pathways, while in turn the deadenylases can regulate the levels of DNA damage-responsive proteins. The mutual feedback between deadenylases and the DDR signaling pathways allows the cells to precisely control DDR by dynamically adjusting the levels of sensors and effectors of the DDR signaling pathways. Here, the diverse functions of deadenylases in DDR are summarized and the underlying mechanisms are proposed according to recent findings. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
Collapse
Affiliation(s)
- Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China
| |
Collapse
|
11
|
Dejene EA, Li Y, Showkatian Z, Ling H, Seto E. Regulation of poly(a)-specific ribonuclease activity by reversible lysine acetylation. J Biol Chem 2020; 295:10255-10270. [PMID: 32457045 DOI: 10.1074/jbc.ra120.012552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN) is a 3'-exoribonuclease that plays an important role in regulating the stability and maturation of RNAs. Recently, PARN has been found to regulate the maturation of the human telomerase RNA component (hTR), a noncoding RNA required for telomere elongation. Specifically, PARN cleaves the 3'-end of immature, polyadenylated hTR to form the mature, nonpolyadenylated template. Despite PARN's critical role in mediating telomere maintenance, little is known about how PARN's function is regulated by post-translational modifications. In this study, using shRNA- and CRISPR/Cas9-mediated gene silencing and knockout approaches, along with 3'-exoribonuclease activity assays and additional biochemical methods, we examined whether PARN is post-translationally modified by acetylation and what effect acetylation has on PARN's activity. We found PARN is primarily acetylated by the acetyltransferase p300 at Lys-566 and deacetylated by sirtuin1 (SIRT1). We also revealed how acetylation of PARN can decrease its enzymatic activity both in vitro, using a synthetic RNA probe, and in vivo, by quantifying endogenous levels of adenylated hTR. Furthermore, we also found that SIRT1 can regulate levels of adenylated hTR through PARN. The findings of our study uncover a mechanism by which PARN acetylation and deacetylation regulate its enzymatic activity as well as levels of mature hTR. Thus, PARN's acetylation status may play a role in regulating telomere length.
Collapse
Affiliation(s)
- Eden A Dejene
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C., USA.,George Washington University Cancer Center, Washington, D.C., USA
| | - Yixuan Li
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C., USA.,George Washington University Cancer Center, Washington, D.C., USA
| | - Zahra Showkatian
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C., USA.,George Washington University Cancer Center, Washington, D.C., USA
| | - Hongbo Ling
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C., USA.,George Washington University Cancer Center, Washington, D.C., USA
| | - Edward Seto
- Department of Biochemistry and Molecular Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C., USA .,George Washington University Cancer Center, Washington, D.C., USA
| |
Collapse
|
12
|
Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1571. [PMID: 31657151 PMCID: PMC7295566 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| |
Collapse
|
13
|
Translation Efficiency and Degradation of ER-Associated mRNAs Modulated by ER-Anchored poly(A)-Specific Ribonuclease (PARN). Cells 2020; 9:cells9010162. [PMID: 31936572 PMCID: PMC7017053 DOI: 10.3390/cells9010162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/05/2020] [Accepted: 01/07/2020] [Indexed: 12/21/2022] Open
Abstract
Translation is spatiotemporally regulated and endoplasmic reticulum (ER)-associated mRNAs are generally in efficient translation. It is unclear whether the ER-associated mRNAs are deadenylated or degraded on the ER surface in situ or in the cytosol. Here, we showed that ER possessed active deadenylases, particularly the poly(A)-specific ribonuclease (PARN), in common cell lines and mouse tissues. Consistently, purified recombinant PARN exhibited a strong ability to insert into the Langmuir monolayer and liposome. ER-anchored PARN was found to be able to reshape the poly(A) length profile of the ER-associated RNAs by suppressing long poly(A) tails without significantly influencing the cytosolic RNAs. The shortening of long poly(A) tails did not affect global translation efficiency, which suggests that the non-specific action of PARN towards long poly(A) tails was beyond the scope of translation regulation on the ER surface. Transcriptome sequencing analysis indicated that the ER-anchored PARN trigged the degradation of a small subset of ER-enriched transcripts. The ER-anchored PARN modulated the translation of its targets by redistributing ribosomes to heavy polysomes, which suggests that PARN might play a role in dynamic ribosome reallocation. During DNA damage response, MK2 phosphorylated PARN-Ser557 to modulate PARN translocation from the ER to cytosol. The ER-anchored PARN modulated DNA damage response and thereby cell viability by promoting the decay of ER-associated MDM2 transcripts with low ribosome occupancy. These findings revealed that highly regulated communication between mRNA degradation rate and translation efficiency is present on the ER surface in situ and PARN might contribute to this communication by modulating the dynamic ribosome reallocation between transcripts with low and high ribosome occupancies.
Collapse
|
14
|
Haronikova L, Olivares-Illana V, Wang L, Karakostis K, Chen S, Fåhraeus R. The p53 mRNA: an integral part of the cellular stress response. Nucleic Acids Res 2019; 47:3257-3271. [PMID: 30828720 PMCID: PMC6468297 DOI: 10.1093/nar/gkz124] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/12/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
A large number of signalling pathways converge on p53 to induce different cellular stress responses that aim to promote cell cycle arrest and repair or, if the damage is too severe, to induce irreversible senescence or apoptosis. The differentiation of p53 activity towards specific cellular outcomes is tightly regulated via a hierarchical order of post-translational modifications and regulated protein-protein interactions. The mechanisms governing these processes provide a model for how cells optimize the genetic information for maximal diversity. The p53 mRNA also plays a role in this process and this review aims to illustrate how protein and RNA interactions throughout the p53 mRNA in response to different signalling pathways control RNA stability, translation efficiency or alternative initiation of translation. We also describe how a p53 mRNA platform shows riboswitch-like features and controls the rate of p53 synthesis, protein stability and modifications of the nascent p53 protein. A single cancer-derived synonymous mutation disrupts the folding of this platform and prevents p53 activation following DNA damage. The role of the p53 mRNA as a target for signalling pathways illustrates how mRNA sequences have co-evolved with the function of the encoded protein and sheds new light on the information hidden within mRNAs.
Collapse
Affiliation(s)
- Lucia Haronikova
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Vanesa Olivares-Illana
- Laboratorio de Interacciones Biomoleculares y cáncer. Instituto de Física Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona universitaria, 78290 SLP, México
| | - Lixiao Wang
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden
| | - Robin Fåhraeus
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic.,Department of Medical Biosciences, Umeå University, 90185 Umeå, Sweden.,Inserm U1162, 27 rue Juliette Dodu, 75010 Paris, France.,ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| |
Collapse
|
15
|
Baquero J, Varriano S, Ordonez M, Kuczaj P, Murphy MR, Aruggoda G, Lundine D, Morozova V, Makki AE, Alonso ADC, Kleiman FE. Nuclear Tau, p53 and Pin1 Regulate PARN-Mediated Deadenylation and Gene Expression. Front Mol Neurosci 2019; 12:242. [PMID: 31749682 PMCID: PMC6843027 DOI: 10.3389/fnmol.2019.00242] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/20/2019] [Indexed: 12/17/2022] Open
Abstract
While nuclear tau plays a role in DNA damage response (DDR) and chromosome relaxation, the mechanisms behind these functions are not fully understood. Here, we show that tau forms complex(es) with factors involved in nuclear mRNA processing such as tumor suppressor p53 and poly(A)-specific ribonuclease (PARN) deadenylase. Tau induces PARN activity in different cellular models during DDR, and this activation is further increased by p53 and inhibited by tau phosphorylation at residues implicated in neurological disorders. Tau's binding factor Pin1, a mitotic regulator overexpressed in cancer and depleted in Alzheimer's disease (AD), also plays a role in the activation of nuclear deadenylation. Tau, Pin1 and PARN target the expression of mRNAs deregulated in AD and/or cancer. Our findings identify novel biological roles of tau and toxic effects of hyperphosphorylated-tau. We propose a model in which factors involved in cancer and AD regulate gene expression by interactions with the mRNA processing machinery, affecting the transcriptome and suggesting insights into alternative mechanisms for the initiation and/or developments of these diseases.
Collapse
Affiliation(s)
- Jorge Baquero
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Sophia Varriano
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Martha Ordonez
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Pawel Kuczaj
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Michael R. Murphy
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Gamage Aruggoda
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Devon Lundine
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| | - Viktoriya Morozova
- Department of Biology and Center for Developmental Neuroscience, College of Staten Island, Graduate Center, The City University of New York, Staten Island, NY, United States
| | - Ali Elhadi Makki
- Department of Biology and Center for Developmental Neuroscience, College of Staten Island, Graduate Center, The City University of New York, Staten Island, NY, United States
| | - Alejandra del C. Alonso
- Department of Biology and Center for Developmental Neuroscience, College of Staten Island, Graduate Center, The City University of New York, Staten Island, NY, United States
| | - Frida E. Kleiman
- Chemistry Department, Hunter College and Biochemistry Program, The Graduate Center, The City University of New York, New York, NY, United States
| |
Collapse
|
16
|
Son A, Park JE, Kim VN. PARN and TOE1 Constitute a 3' End Maturation Module for Nuclear Non-coding RNAs. Cell Rep 2019; 23:888-898. [PMID: 29669292 DOI: 10.1016/j.celrep.2018.03.089] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 12/27/2017] [Accepted: 03/20/2018] [Indexed: 10/17/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN) and target of EGR1 protein 1 (TOE1) are nuclear granule-associated deadenylases, whose mutations are linked to multiple human diseases. Here, we applied mTAIL-seq and RNA sequencing (RNA-seq) to systematically identify the substrates of PARN and TOE1 and elucidate their molecular functions. We found that PARN and TOE1 do not modulate the length of mRNA poly(A) tails. Rather, they promote the maturation of nuclear small non-coding RNAs (ncRNAs). PARN and TOE1 act redundantly on some ncRNAs, most prominently small Cajal body-specific RNAs (scaRNAs). scaRNAs are strongly downregulated when PARN and TOE1 are compromised together, leading to defects in small nuclear RNA (snRNA) pseudouridylation. They also function redundantly in the biogenesis of telomerase RNA component (TERC), which shares sequence motifs found in H/ACA box scaRNAs. Our findings extend the knowledge of nuclear ncRNA biogenesis, and they provide insights into the pathology of PARN/TOE1-associated genetic disorders whose therapeutic treatments are currently unavailable.
Collapse
Affiliation(s)
- Ahyeon Son
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Eun Park
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
| |
Collapse
|
17
|
Mironova N, Vlassov V. Surveillance of Tumour Development: The Relationship Between Tumour-Associated RNAs and Ribonucleases. Front Pharmacol 2019; 10:1019. [PMID: 31572192 PMCID: PMC6753386 DOI: 10.3389/fphar.2019.01019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/09/2019] [Indexed: 12/14/2022] Open
Abstract
Tumour progression is accompanied by rapid cell proliferation, loss of differentiation, the reprogramming of energy metabolism, loss of adhesion, escape of immune surveillance, induction of angiogenesis, and metastasis. Both coding and regulatory RNAs expressed by tumour cells and circulating in the blood are involved in all stages of tumour progression. Among the important tumour-associated RNAs are intracellular coding RNAs that determine the routes of metabolic pathways, cell cycle control, angiogenesis, adhesion, apoptosis and pathways responsible for transformation, and intracellular and extracellular non-coding RNAs involved in regulation of the expression of their proto-oncogenic and oncosuppressing mRNAs. Considering the diversity/variability of biological functions of RNAs, it becomes evident that extracellular RNAs represent important regulators of cell-to-cell communication and intracellular cascades that maintain cell proliferation and differentiation. In connection with the elucidation of such an important role for RNA, a surge in interest in RNA-degrading enzymes has increased. Natural ribonucleases (RNases) participate in various cellular processes including miRNA biogenesis, RNA decay and degradation that has determined their principal role in the sustention of RNA homeostasis in cells. Findings were obtained on the contribution of some endogenous ribonucleases in the maintenance of normal cell RNA homeostasis, which thus prevents cell transformation. These findings directed attention to exogenous ribonucleases as tools to compensate for the malfunction of endogenous ones. Recently a number of proteins with ribonuclease activity were discovered whose intracellular function remains unknown. Thus, the comprehensive investigation of physiological roles of RNases is still required. In this review we focused on the control mechanisms of cell transformation by endogenous ribonucleases, and the possibility of replacing malfunctioning enzymes with exogenous ones.
Collapse
Affiliation(s)
- Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| |
Collapse
|
18
|
Duan TL, He GJ, Hu LD, Yan YB. The Intrinsically Disordered C-Terminal Domain Triggers Nucleolar Localization and Function Switch of PARN in Response to DNA Damage. Cells 2019; 8:cells8080836. [PMID: 31387300 PMCID: PMC6721724 DOI: 10.3390/cells8080836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/23/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
Poly(A)-specific ribonuclease (PARN), a multifunctional multi-domain deadenylase, is crucial to the regulation of mRNA turnover and the maturation of various non-coding RNAs. Despite extensive studies of the well-folding domains responsible for PARN catalysis, the structure and function of the C-terminal domain (CTD) remains elusive. PARN is a cytoplasm-nucleus shuttle protein with concentrated nucleolar distribution. Here, we identify the nuclear and nucleolar localization signals in the CTD of PARN. Spectroscopic studies indicated that PARN-CTD is intrinsically disordered with loosely packed local structures/tertiary structure. Phosphorylation-mimic mutation S557D disrupted the local structure and facilitated the binding of the CTD with the well-folded domains, with no impact on PARN deadenylase activity. Under normal conditions, the nucleolus-residing PARN recruited CBP80 into the nucleoli to repress its deadenylase activity, while DNA damage-induced phosphorylation of PARN-S557 expelled CBP80 from the nucleoli to discharge activity inhibition and attracted nucleoplasm-located CstF-50 into the nucleoli to activate deadenylation. The structure switch-induced function switch of PARN reshaped the profile of small nuclear non-coding RNAs to respond to DNA damage. Our findings highlight that the structure switch of the CTD induced by posttranslational modifications redefines the subset of binding partners, and thereby the RNA targets in the nucleoli.
Collapse
Affiliation(s)
- Tian-Li Duan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guang-Jun He
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li-Dan Hu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
19
|
Abshire ET, Chasseur J, Bohn JA, Del Rizzo PA, Freddolino PL, Goldstrohm AC, Trievel RC. The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells. Nucleic Acids Res 2019; 46:6257-6270. [PMID: 29860338 PMCID: PMC6158716 DOI: 10.1093/nar/gky412] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/09/2018] [Indexed: 12/22/2022] Open
Abstract
The circadian protein Nocturnin (NOCT) belongs to the exonuclease, endonuclease and phosphatase superfamily and is most similar to the CCR4-class of deadenylases that degrade the poly-adenosine tails of mRNAs. NOCT-deficient mice are resistant to high-fat diet induced weight gain, and exhibit dysregulation of bone formation. However, the mechanisms by which NOCT regulates these processes remain to be determined. Here, we describe a pair of high-resolution crystal structures of the human NOCT catalytic domain. The active site of NOCT is highly conserved with other exoribonucleases, and when directed to a transcript in cells, NOCT can reduce translation and abundance of that mRNA in a manner dependent on key active site residues. In contrast to the related deadenylase CNOT6L, purified recombinant NOCT lacks in vitro ribonuclease activity, suggesting that unidentified factors are necessary for enzymatic activity. We also find the ability of NOCT to repress reporter mRNAs in cells depends upon the 3' end of the mRNA, as reporters terminating with a 3' MALAT1 structure cannot be repressed by NOCT. Together, these data demonstrate that NOCT is an exoribonuclease that can degrade mRNAs to inhibit protein expression, suggesting a molecular mechanism for its regulatory role in lipid metabolism and bone development.
Collapse
Affiliation(s)
- Elizabeth T Abshire
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer Chasseur
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A Bohn
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul A Del Rizzo
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
20
|
Kim M, Zhang X. The Profiling and Role of miRNAs in Diabetes Mellitus. JOURNAL OF DIABETES AND CLINICAL RESEARCH 2019; 1:5-23. [PMID: 32432227 PMCID: PMC7236805 DOI: 10.33696/diabetes.1.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Diabetes mellitus (DM), a complex metabolic disease, has become a global threat to human health worldwide. Over the past decades, an enormous amount of effort has been devoted to understand how microRNAs (miRNAs), a class of small non-coding RNA regulators of gene expression at the post-transcriptional level, are implicated in DM pathology. Growing evidence suggests that the expression signature of a specific set of miRNAs has been altered in the progression of DM. In the present review, we summarize the recent investigations on the miRNA profiles as novel DM biomarkers in clinical studies and in animal models, and highlight recent discoveries on the complex regulatory effect and functional role of miRNAs in DM.
Collapse
Affiliation(s)
- Michael Kim
- Department of Medicine, Division of Cardiology, Columbia University Medical Center, New York, NY, USA
| | - Xiaokan Zhang
- Department of Medicine, Division of Cardiology, Columbia University Medical Center, New York, NY, USA
| |
Collapse
|
21
|
Benyelles M, Episkopou H, O'Donohue M, Kermasson L, Frange P, Poulain F, Burcu Belen F, Polat M, Bole‐Feysot C, Langa‐Vives F, Gleizes P, de Villartay J, Callebaut I, Decottignies A, Revy P. Impaired telomere integrity and rRNA biogenesis in PARN-deficient patients and knock-out models. EMBO Mol Med 2019; 11:e10201. [PMID: 31273937 PMCID: PMC6609912 DOI: 10.15252/emmm.201810201] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/24/2019] [Accepted: 05/09/2019] [Indexed: 12/12/2022] Open
Abstract
PARN, poly(A)-specific ribonuclease, regulates the turnover of mRNAs and the maturation and stabilization of the hTR RNA component of telomerase. Biallelic PARN mutations were associated with Høyeraal-Hreidarsson (HH) syndrome, a rare telomere biology disorder that, because of its severity, is likely not exclusively due to hTR down-regulation. Whether PARN deficiency was affecting the expression of telomere-related genes was still unclear. Using cells from two unrelated HH individuals carrying novel PARN mutations and a human PARN knock-out (KO) cell line with inducible PARN complementation, we found that PARN deficiency affects both telomere length and stability and down-regulates the expression of TRF1, TRF2, TPP1, RAP1, and POT1 shelterin transcripts. Down-regulation of dyskerin-encoding DKC1 mRNA was also observed and found to result from p53 activation in PARN-deficient cells. We further showed that PARN deficiency compromises ribosomal RNA biogenesis in patients' fibroblasts and cells from heterozygous Parn KO mice. Homozygous Parn KO however resulted in early embryonic lethality that was not overcome by p53 KO. Our results refine our knowledge on the pleiotropic cellular consequences of PARN deficiency.
Collapse
Affiliation(s)
- Maname Benyelles
- Laboratory of Genome Dynamics in the Immune SystemINSERM, UMR 1163ParisFrance
- Laboratoire labellisé LigueImagine InstituteParis Descartes–Sorbonne Paris Cite UniversityParisFrance
| | | | - Marie‐Françoise O'Donohue
- Laboratoire de Biologie Moléculaire EucaryoteCentre de Biologie Intégrative (CBI)CNRS, UPSUniversité de ToulouseToulouseFrance
| | - Laëtitia Kermasson
- Laboratory of Genome Dynamics in the Immune SystemINSERM, UMR 1163ParisFrance
- Laboratoire labellisé LigueImagine InstituteParis Descartes–Sorbonne Paris Cite UniversityParisFrance
| | - Pierre Frange
- EA 7327, Université Paris Descartes, Sorbonne Paris‐CitéParisFrance
- Laboratoire de Microbiologie clinique & Unité d'ImmunologieHématologie et Rhumatologie PédiatriquesAP‐HP, Hôpital Necker, Enfants MaladesParisFrance
| | - Florian Poulain
- de Duve InstituteUniversité catholique de LouvainBrusselsBelgium
| | - Fatma Burcu Belen
- Pediatric HematologyFaculty of MedicineBaskent UniversityAnkaraTurkey
| | - Meltem Polat
- Pediatric Infectious DiseasesDepartment of Pediatric Infectious DiseasesPamukkale University Medical FacultyDenizliTurkey
| | - Christine Bole‐Feysot
- INSERM, UMR 1163Genomics platform, Imagine InstituteParis Descartes–Sorbonne Paris Cité UniversityParisFrance
- Genomic Core FacilityImagine Institute‐Structure Fédérative de Recherche NeckerINSERM U1163ParisFrance
| | | | - Pierre‐Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire EucaryoteCentre de Biologie Intégrative (CBI)CNRS, UPSUniversité de ToulouseToulouseFrance
| | - Jean‐Pierre de Villartay
- Laboratory of Genome Dynamics in the Immune SystemINSERM, UMR 1163ParisFrance
- Laboratoire labellisé LigueImagine InstituteParis Descartes–Sorbonne Paris Cite UniversityParisFrance
| | - Isabelle Callebaut
- Muséum National d'Histoire NaturelleUMR CNRS 7590Institut de Minéralogiede Physique des Matériaux et de Cosmochimie, IMPMCSorbonne UniversitéParisFrance
| | | | - Patrick Revy
- Laboratory of Genome Dynamics in the Immune SystemINSERM, UMR 1163ParisFrance
- Laboratoire labellisé LigueImagine InstituteParis Descartes–Sorbonne Paris Cite UniversityParisFrance
| |
Collapse
|
22
|
Curtale G, Rubino M, Locati M. MicroRNAs as Molecular Switches in Macrophage Activation. Front Immunol 2019; 10:799. [PMID: 31057539 PMCID: PMC6478758 DOI: 10.3389/fimmu.2019.00799] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/26/2019] [Indexed: 12/25/2022] Open
Abstract
The efficacy of macrophage- mediated inflammatory response relies on the coordinated expression of key factors, which expression is finely regulated at both transcriptional and post-transcriptional level. Several studies have provided compelling evidence that microRNAs play pivotal roles in modulating macrophage activation, polarization, tissue infiltration, and resolution of inflammation. In this review, we highlight the essential molecular mechanisms underlying the different phases of inflammation that are targeted by microRNAs to inhibit or accelerate restoration to tissue integrity and homeostasis. We further review the impact of microRNA-dependent regulation of tumor-associated macrophages and the relative implication for tumor biology.
Collapse
Affiliation(s)
- Graziella Curtale
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy.,Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Marcello Rubino
- Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Massimo Locati
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy.,Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| |
Collapse
|
23
|
Gomez-Cambronero J. Lack of effective translational regulation of PLD expression and exosome biogenesis in triple-negative breast cancer cells. Cancer Metastasis Rev 2019; 37:491-507. [PMID: 30091053 DOI: 10.1007/s10555-018-9753-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that is difficult to treat since cells lack the three receptors (ES, PR, or HER) that the most effective treatments target. We have used a well-established TNBC cell line (MDA-MB-231) from which we found evidence in support for a phospholipase D (PLD)-mediated tumor growth and metastasis: high levels of expression of PLD, as well as the absence of inhibitory miRs (such as miR-203) and 3'-mRNA PARN deadenylase activity in these cells. Such findings are not present in a luminal B cell line, MCF-7, and we propose a new miR•PARN•PLD node that is not uniform across breast cancer molecular subtypes and as such TNBC could be pharmacologically targeted differentially. We review the participation of PLD and phosphatidic acid (PA), its enzymatic product, as new "players" in breast cancer biology, with the aspects of regulation of the tumor microenvironment, macrophage polarization, regulation of PLD transcripts by specific miRs and deadenylases, and PLD-regulated exosome biogenesis. A new signaling miR•PARN•PLD node could serve as new biomarkers for TNBC abnormal signaling and metastatic disease staging, potentially before metastases are able to be visualized using conventional imaging.
Collapse
Affiliation(s)
- Julian Gomez-Cambronero
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, 3640 Colonel Glenn Highway, Dayton, OH, 45435, USA.
| |
Collapse
|
24
|
Shukla S, Bjerke GA, Muhlrad D, Yi R, Parker R. The RNase PARN Controls the Levels of Specific miRNAs that Contribute to p53 Regulation. Mol Cell 2019; 73:1204-1216.e4. [PMID: 30770239 DOI: 10.1016/j.molcel.2019.01.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 11/08/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022]
Abstract
PARN loss-of-function mutations cause a severe form of the hereditary disease dyskeratosis congenita (DC). PARN deficiency affects the stability of non-coding RNAs such as human telomerase RNA (hTR), but these effects do not explain the severe disease in patients. We demonstrate that PARN deficiency affects the levels of numerous miRNAs in human cells. PARN regulates miRNA levels by stabilizing either mature or precursor miRNAs by removing oligo(A) tails added by the poly(A) polymerase PAPD5, which if remaining recruit the exonuclease DIS3L or DIS3L2 to degrade the miRNA. PARN knockdown destabilizes multiple miRNAs that repress p53 translation, which leads to an increase in p53 accumulation in a Dicer-dependent manner, thus explaining why PARN-defective patients show p53 accumulation. This work also reveals that DIS3L and DIS3L2 are critical 3' to 5' exonucleases that regulate miRNA stability, with the addition and removal of 3' end extensions controlling miRNA levels in the cell.
Collapse
Affiliation(s)
- Siddharth Shukla
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Glen A Bjerke
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Denise Muhlrad
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Rui Yi
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| |
Collapse
|
25
|
Chen EYY, Chen JS, Ying SY. The microRNA and the perspectives of miR-302. Heliyon 2019; 5:e01167. [PMID: 30723835 PMCID: PMC6351428 DOI: 10.1016/j.heliyon.2019.e01167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/18/2018] [Accepted: 01/22/2019] [Indexed: 12/24/2022] Open
Abstract
MiRNAs are naturally occurring, small, non-coding RNA molecules that post-transcriptionally regulate the expression of a large number of genes involved in various biological processes, either through mRNA degradation or through translation inhibition. MiRNAs play important roles in many aspects of physiology and pathology throughout the body, particularly in cancer, which have made miRNAs attractive tools and targets for translational research. The types of non-coding RNAs, biogenesis of miRNAs, circulating miRNAs, and direct delivery of miRNA were briefly reviewed. As a case of point, the role and perspective of miR-302, a family of ES-specific miRNA, on cancer, iPSCs, heart disease were presented.
Collapse
Affiliation(s)
- Emily Yen Yu Chen
- Department of Integrative Anatomical Sciences, Keck School of Medicine, BMT-403, University of Southern California, 1333 San Pablo Street, Los Angeles, CA 90033, USA
- WJWU & LYNN Institute for Stem Cell Research, Santa Fe Springs, CA 90670, USA
| | - Jack S. Chen
- WJWU & LYNN Institute for Stem Cell Research, Santa Fe Springs, CA 90670, USA
| | - Shao-Yao Ying
- Department of Integrative Anatomical Sciences, Keck School of Medicine, BMT-403, University of Southern California, 1333 San Pablo Street, Los Angeles, CA 90033, USA
| |
Collapse
|
26
|
Gong Y, Ju C, Zhang X. Shrimp miR-1000 Functions in Antiviral Immunity by Simultaneously Triggering the Degradation of Two Viral mRNAs. Front Immunol 2018; 9:2999. [PMID: 30619352 PMCID: PMC6305465 DOI: 10.3389/fimmu.2018.02999] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) function as crucial suppressors of gene expression via translational repression or direct mRNA degradation. However, the mechanism of multi-gene regulation by a host miRNA in antiviral immunity has not been extensively explored. In this study, the regulation of two white spot syndrome virus (WSSV) genes by its host (Marsupenaeus japonicus shrimp) miRNA (shrimp miR-1000) was characterized. The miRNA target gene prediction showed that only two virus genes (wsv191 and wsv407) might be the targets of miR-1000. The results of insect cell transfection assays revealed that shrimp miR-1000 could target multiple virus genes (wsv191 and wsv407). The mRNA degradation analysis and RNA FISH (fluorescence in situ hybridization) analysis indicated that miR-1000 triggered the mRNA degradation of target genes through 5′-3′ exonucleolytic digestion in vivo and thereby inhibited the virus infection in shrimp. The miRNA-mediated 5′-3′ exonucleolytic digestion of target mRNAs stopped near the 3′UTR (3′untranslated region) sequence complementary to the seed sequence of miR-1000. Therefore, our study provided novel insights into how a host miRNA targeted multiple viral genes and prevented host from virus infection.
Collapse
Affiliation(s)
- Yi Gong
- Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chenyu Ju
- Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaobo Zhang
- Laboratory for Marine Biology and Biotechnology of Qingdao National Laboratory for Marine Science and Technology, College of Life Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
27
|
Beta RAA, Balatsos NAA. Tales around the clock: Poly(A) tails in circadian gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1484. [PMID: 29911349 DOI: 10.1002/wrna.1484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 04/15/2018] [Accepted: 04/20/2018] [Indexed: 11/07/2022]
Abstract
Circadian rhythms are ubiquitous time-keeping processes in eukaryotes with a period of ~24 hr. Light is perhaps the main environmental cue (zeitgeber) that affects several aspects of physiology and behaviour, such as sleep/wake cycles, orientation of birds and bees, and leaf movements in plants. Temperature can serve as the main zeitgeber in the absence of light cycles, even though it does not lead to rhythmicity through the same mechanism as light. Additional cues include feeding patterns, humidity, and social rhythms. At the molecular level, a master oscillator orchestrates circadian rhythms and organizes molecular clocks located in most cells. The generation of the 24 hr molecular clock is based on transcriptional regulation, as it drives intrinsic rhythmic changes based on interlocked transcription/translation feedback loops that synchronize expression of genes. Thus, processes and factors that determine rhythmic gene expression are important to understand circadian rhythms. Among these, the poly(A) tails of RNAs play key roles in their stability, translational efficiency and degradation. In this article, we summarize current knowledge and discuss perspectives on the role and significance of poly(A) tails and associating factors in the context of the circadian clock. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA Processing > 3' End Processing.
Collapse
Affiliation(s)
- Rafailia A A Beta
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| |
Collapse
|
28
|
The Guardian of the Genome Revisited: p53 Downregulates Genes Required for Telomere Maintenance, DNA Repair, and Centromere Structure. Cancers (Basel) 2018; 10:cancers10050135. [PMID: 29734785 PMCID: PMC5977108 DOI: 10.3390/cancers10050135] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 02/06/2023] Open
Abstract
The p53 protein has been extensively studied for its capacity to prevent proliferation of cells with a damaged genome. Surprisingly, however, our recent analysis of mice expressing a hyperactive mutant p53 that lacks the C-terminal domain revealed that increased p53 activity may alter genome maintenance. We showed that p53 downregulates genes essential for telomere metabolism, DNA repair, and centromere structure and that a sustained p53 activity leads to phenotypic traits associated with dyskeratosis congenita and Fanconi anemia. This downregulation is largely conserved in human cells, which suggests that our findings could be relevant to better understand processes involved in bone marrow failure as well as aging and tumor suppression.
Collapse
|
29
|
Johnson JM, Thürich J, Petutschnig EK, Altschmied L, Meichsner D, Sherameti I, Dindas J, Mrozinska A, Paetz C, Scholz SS, Furch ACU, Lipka V, Hedrich R, Schneider B, Svatoš A, Oelmüller R. A Poly(A) Ribonuclease Controls the Cellotriose-Based Interaction between Piriformospora indica and Its Host Arabidopsis. PLANT PHYSIOLOGY 2018; 176:2496-2514. [PMID: 29371249 PMCID: PMC5841714 DOI: 10.1104/pp.17.01423] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/12/2018] [Indexed: 05/17/2023]
Abstract
Piriformospora indica, an endophytic root-colonizing fungus, efficiently promotes plant growth and induces resistance to abiotic stress and biotic diseases. P. indica fungal cell wall extract induces cytoplasmic calcium elevation in host plant roots. Here, we show that cellotriose (CT) is an elicitor-active cell wall moiety released by P. indica into the medium. CT induces a mild defense-like response, including the production of reactive oxygen species, changes in membrane potential, and the expression of genes involved in growth regulation and root development. CT-based cytoplasmic calcium elevation in Arabidopsis (Arabidopsis thaliana) roots does not require the BAK1 coreceptor or the putative Ca2+ channels TPC1, GLR3.3, GLR2.4, and GLR2.5 and operates synergistically with the elicitor chitin. We identified an ethyl methanesulfonate-induced mutant (cytoplasmiccalcium elevation mutant) impaired in the response to CT and various other cellooligomers (n = 2-7), but not to chitooligomers (n = 4-8), in roots. The mutant contains a single nucleotide exchange in the gene encoding a poly(A) ribonuclease (AtPARN; At1g55870) that degrades the poly(A) tails of specific mRNAs. The wild-type PARN cDNA, expressed under the control of a 35S promoter, complements the mutant phenotype. Our identification of cellotriose as a novel chemical mediator casts light on the complex P. indica-plant mutualistic relationship.
Collapse
Affiliation(s)
- Joy M Johnson
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics, and Molecular Botany, Friedrich-Schiller-University, D-07743 Jena, Germany
| | - Johannes Thürich
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics, and Molecular Botany, Friedrich-Schiller-University, D-07743 Jena, Germany
| | - Elena K Petutschnig
- Department of Plant Cell Biology, Albrecht von Haller Institute, Georg August University, 37077 Goettingen, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, 06466 Stadt Seeland, Germany
| | - Doreen Meichsner
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics, and Molecular Botany, Friedrich-Schiller-University, D-07743 Jena, Germany
| | - Irena Sherameti
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics, and Molecular Botany, Friedrich-Schiller-University, D-07743 Jena, Germany
| | - Julian Dindas
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, University of Würzburg, D-97082 Wuerzburg, Germany
| | - Anna Mrozinska
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics, and Molecular Botany, Friedrich-Schiller-University, D-07743 Jena, Germany
| | - Christian Paetz
- Research Group Biosynthesis/NMR, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Sandra S Scholz
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics, and Molecular Botany, Friedrich-Schiller-University, D-07743 Jena, Germany
| | - Alexandra C U Furch
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics, and Molecular Botany, Friedrich-Schiller-University, D-07743 Jena, Germany
| | - Volker Lipka
- Department of Plant Cell Biology, Albrecht von Haller Institute, Georg August University, 37077 Goettingen, Germany
| | - Rainer Hedrich
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, University of Würzburg, D-97082 Wuerzburg, Germany
| | - Bernd Schneider
- Research Group Biosynthesis/NMR, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics, and Molecular Botany, Friedrich-Schiller-University, D-07743 Jena, Germany
| |
Collapse
|
30
|
Zhang X, Xiao S, Rameau RD, Devany E, Nadeem Z, Caglar E, Ng K, Kleiman FE, Saxena A. Nucleolin phosphorylation regulates PARN deadenylase activity during cellular stress response. RNA Biol 2018; 15:251-260. [PMID: 29168431 PMCID: PMC5798948 DOI: 10.1080/15476286.2017.1408764] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/11/2017] [Accepted: 11/16/2017] [Indexed: 01/28/2023] Open
Abstract
Nucleolin (NCL) is an abundant stress-responsive, RNA-binding phosphoprotein that controls gene expression by regulating either mRNA stability and/or translation. NCL binds to the AU-rich element (ARE) in the 3'UTR of target mRNAs, mediates miRNA functions in the nearby target sequences, and regulates mRNA deadenylation. However, the mechanism by which NCL phosphorylation affects these functions and the identity of the deadenylase involved, remain largely unexplored. Earlier we demonstrated that NCL phosphorylation is vital for cell cycle progression and proliferation, whereas phosphorylation-deficient NCL at six consensus CK2 sites confers dominant-negative effect on proliferation by increasing p53 expression, possibly mimicking cellular DNA damage conditions. In this study, we show that NCL phosphorylation at those CK2 consensus sites in the N-terminus is necessary to induce deadenylation upon oncogenic stimuli and UV stress. NCL-WT, but not hypophosphorylated NCL-6/S*A, activates poly (A)-specific ribonuclease (PARN) deadenylase activity. We further demonstrate that NCL interacts directly with PARN, and under non-stress conditions also forms (a) complex (es) with factors that regulate deadenylation, such as p53 and the ARE-binding protein HuR. Upon UV stress, the interaction of hypophosphorylated NCL-6/S*A with these proteins is favored. As an RNA-binding protein, NCL interacts with PARN deadenylase substrates such as TP53 and BCL2 mRNAs, playing a role in their downregulation under non-stress conditions. For the first time, we show that NCL phosphorylation offers specificity to its protein-protein, protein-RNA interactions, resulting in the PARN deadenylase regulation, and hence gene expression, during cellular stress responses.
Collapse
Affiliation(s)
- Xiaokan Zhang
- Chemistry Department, Hunter College, New York, NY, USA
| | - Shu Xiao
- Biology Department, Brooklyn College, Brooklyn, NY, USA
| | | | - Emral Devany
- Chemistry Department, Hunter College, New York, NY, USA
| | - Zaineb Nadeem
- Biology Department, Brooklyn College, Brooklyn, NY, USA
| | - Elif Caglar
- Biology Department, Brooklyn College, Brooklyn, NY, USA
| | - Kenneth Ng
- Biology Department, Brooklyn College, Brooklyn, NY, USA
| | | | - Anjana Saxena
- Biology Department, Brooklyn College, Brooklyn, NY, USA
| |
Collapse
|
31
|
Abstract
MicroRNAs (miRNAs), widely distributed, small regulatory RNA genes, target both messenger RNA (mRNA) degradation and suppression of protein translation based on sequence complementarity between the miRNA and its targeted mRNA. Different names have been used to describe various types of miRNA. During evolution, RNA retroviruses or transgenes invaded the eukaryotic genome and were inserted itself in the noncoding regions of DNA, conceivably acting as transposon-like jumping genes, providing defense from viral invasion and fine-tuning of gene expression as a secondary level of gene modulation in eukaryotes. When a transposon is inserted in the intron, it becomes an intronic miRNA, taking advantage of the protein synthesis machinery, i.e., mRNA transcription and splicing, as a means for processing and maturation. MiRNAs have been found to play an important, but not life-threatening, role in embryonic development. They might play a pivotal role in diverse biological systems in various organisms, facilitating a quick response and accurate plotting of body physiology and structures. Based on these unique properties, manufactured intronic miRNAs have been developed for in vitro evaluation of gene function, in vivo gene therapy, and generation of transgenic animal models. The biogenesis of miRNAs, circulating miRNAs, miRNAs and cancer, iPSCs, and heart disease are presented in this chapter, highlighting some recent studies on these topics.
Collapse
Affiliation(s)
- Shao-Yao Ying
- Department of Integrative Anatomical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Donald C Chang
- WJWU & LYNN Institute for Stem Cell Research, Santa Fe Springs, CA, USA
| | - Shi-Lung Lin
- Division of Regenerative Medicine, WJWU & LYNN Institute for Stem Cell Research, Santa Fe Springs, CA, USA
| |
Collapse
|
32
|
Skeparnias I, Αnastasakis D, Shaukat AN, Grafanaki K, Stathopoulos C. Expanding the repertoire of deadenylases. RNA Biol 2017; 14:1320-1325. [PMID: 28267419 PMCID: PMC5711463 DOI: 10.1080/15476286.2017.1300222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/13/2017] [Accepted: 02/23/2017] [Indexed: 12/20/2022] Open
Abstract
Deadenylases belong to an expanding family of exoribonucleases involved mainly in mRNA stability and turnover, with the exception of PARN which has additional roles in the biogenesis of several important non-coding RNAs, including miRNAs and piRNAs. Recently, PARN in C. elegans and its homolog PNLDC1 in B. mori were reported as the elusive trimmers mediating piRNA biogenesis. In addition, characterization of mammalian PNLDC1 in comparison to PARN, showed that is specifically expressed in embryonic stem and germ cells, as well as during early embryo development. Moreover, its expression is correlated with epigenetic events mediated by the de novo DNMT3b methyltransferase and knockdown in stem cells upregulates important genes that regulate multipotency. The recent data suggest that at least some new deadenylases may have expanded roles in cell metabolism as regulators of gene expression, through mRNA deadenylation, ncRNAs biogenesis and ncRNA-mediated mRNA targeting, linking essential mechanisms that regulate epigenetic control and transition events during differentiation. The possible roles of mammalian PNLDC1 along those dynamic networks are discussed in the light of new extremely important findings.
Collapse
Affiliation(s)
- Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, Greece
| | | | | | - Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, Greece
| | | |
Collapse
|
33
|
Gomez-Cambronero J, Fite K, Miller TE. How miRs and mRNA deadenylases could post-transcriptionally regulate expression of tumor-promoting protein PLD. Adv Biol Regul 2017; 68:107-119. [PMID: 28964725 DOI: 10.1016/j.jbior.2017.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 12/11/2022]
Abstract
Phospholipase D (PLD) plays a key role in both cell membrane lipid reorganization and architecture, as well as a cell signaling protein via the product of its enzymatic reaction, phosphatidic acid (PA). PLD is involved in promoting breast cancer cell growth, proliferation, and metastasis and both gene and protein expression are upregulated in breast carcinoma human samples. In spite of all this, the ultimate reason as to why PLD expression is high in cancer cells vs. their normal counterparts remains largely unknown. Until we understand this and the associated signaling pathways, it will be difficult to establish PLD as a bona fide target to explore new potential cancer therapeutic approaches. Recently, our lab has identified several molecular mechanisms by which PLD expression is high in breast cancer cells and they all involve post-transcriptional control of its mRNA. First, PA, a mitogen, functions as a protein and mRNA stabilizer that counteracts natural decay and degradation. Second, there is a repertoire of microRNAs (miRs) that keep PLD mRNA translation at low levels in normal cells, but their effects change with starvation and during endothelial-to-mesenchymal transition (EMT) in cancer cells. Third, there is a novel way of post-transcriptional regulation of PLD involving 3'-exonucleases, specifically the deadenylase, Poly(A)-specific Ribonuclease (PARN), which tags mRNA for mRNA for degradation. This would enable PLD accumulation and ultimately breast cancer cell growth. We review in depth the emerging field of post-transcriptional regulation of PLD, which is only recently beginning to be understood. Since, surprisingly, so little is known about post-transcriptional regulation of PLD and related phospholipases (PLC or PLA), this new knowledge could help our understanding of how post-transcriptional deregulation of a lipid enzyme expression impacts tumor growth.
Collapse
Affiliation(s)
- Julian Gomez-Cambronero
- Wright State University School of Medicine, Department of Biochemistry and Molecular Biology, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA.
| | - Kristen Fite
- Wright State University School of Medicine, Department of Biochemistry and Molecular Biology, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
| | - Taylor E Miller
- Wright State University School of Medicine, Department of Biochemistry and Molecular Biology, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
| |
Collapse
|
34
|
Miller TE, Gomez-Cambronero J. A feedback mechanism between PLD and deadenylase PARN for the shortening of eukaryotic poly(A) mRNA tails that is deregulated in cancer cells. Biol Open 2017; 6:176-186. [PMID: 28011629 PMCID: PMC5312095 DOI: 10.1242/bio.021261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The removal of mRNA transcript poly(A) tails by 3′→5′ exonucleases is the rate-limiting step in mRNA decay in eukaryotes. Known cellular deadenylases are the CCR4-NOT and PAN complexes, and poly(A)-specific ribonuclease (PARN). The physiological roles and regulation for PARN is beginning to be elucidated. Since phospholipase D (PLD2 isoform) gene expression is upregulated in breast cancer cells and PARN is downregulated, we examined whether a signaling connection existed between these two enzymes. Silencing PARN with siRNA led to an increase in PLD2 protein, whereas overexpression of PARN had the opposite effect. Overexpression of PLD2, however, led to an increase in PARN expression. Thus, PARN downregulates PLD2 whereas PLD2 upregulates PARN. Co-expression of both PARN and PLD2 mimicked this pattern in non-cancerous cells (COS-7 fibroblasts) but, surprisingly, not in breast cancer MCF-7 cells, where PARN switches from inhibition to activation of PLD2 gene and protein expression. Between 30 and 300 nM phosphatidic acid (PA), the product of PLD enzymatic reaction, added exogenously to culture cells had a stabilizing role of both PARN and PLD2 mRNA decay. Lastly, by immunofluorescence microscopy, we observed an intracellular co-localization of PA-loaded vesicles (0.1-1 nm) and PARN. In summary, we report for the first time the involvement of a phospholipase (PLD2) and PA in mediating PARN-induced eukaryotic mRNA decay and the crosstalk between the two enzymes that is deregulated in breast cancer cells. Summary: Cell signaling enzyme phospholipase D2 (PLD2) and its reaction product, phospholipid phosphatidic acid (PA), are involved in mediating PARN-induced eukaryotic mRNA decay.
Collapse
Affiliation(s)
- Taylor E Miller
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, OH 45435, USA
| | - Julian Gomez-Cambronero
- Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA .,Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, OH 45435, USA
| |
Collapse
|
35
|
Newman M, Sfaxi R, Saha A, Monchaud D, Teulade-Fichou MP, Vagner S. The G-Quadruplex-Specific RNA Helicase DHX36 Regulates p53 Pre-mRNA 3'-End Processing Following UV-Induced DNA Damage. J Mol Biol 2016; 429:3121-3131. [PMID: 27940037 DOI: 10.1016/j.jmb.2016.11.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/26/2016] [Accepted: 11/30/2016] [Indexed: 12/17/2022]
Abstract
Pre-mRNA 3'-end processing, the process through which almost all eukaryotic mRNAs acquire a poly(A) tail is generally inhibited during the cellular DNA damage response leading to a profound impact on the level of protein expression since unprocessed transcripts at the 3'-end will be degraded or unable to be transported to the cytoplasm. However, a compensatory mechanism involving the binding of the hnRNP H/F family of RNA binding proteins to an RNA G-quadruplex (G4) structure located in the vicinity of a polyadenylation site has previously been described to allow the transcript encoding the p53 tumour suppressor protein to be properly processed during DNA damage and to provide the cells with a way to react to DNA damage. Here we report that the DEAH (Asp-Glu-Ala-His) box RNA helicase DHX36/RHAU/G4R1, which specifically binds to and resolves parallel-stranded G4, is necessary to maintain p53 pre-mRNA 3'-end processing following UV-induced DNA damage. DHX36 binds to the p53 RNA G4, while mutation of the G4 impairs the ability of DHX36 to maintain pre-mRNA 3'-end processing. Stabilization of the p53 RNA G4 with two different G4 ligands (PNADOTASQ and PhenDC3), which is expected from previous studies to prevent DHX36 from binding and unwinding G4s, also impairs p53 pre-mRNA 3'-end processing following UV. Our work identifies DHX36 as a new actor in the compensatory mechanisms that are in place to ensure that the mRNAs encoding p53 are still processed following UV.
Collapse
Affiliation(s)
- Michelle Newman
- Institut Curie, PSL Research University, CNRS UMR3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, F-91405 Orsay, France; Equipe Labellisée Ligue Contre le Cancer, F-91405 Orsay, France
| | - Rym Sfaxi
- Institut Curie, PSL Research University, CNRS UMR3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, F-91405 Orsay, France; Equipe Labellisée Ligue Contre le Cancer, F-91405 Orsay, France
| | - Abhijit Saha
- Institut Curie, PSL Research University, CNRS UMR9187-INSERM U1196, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, UMR9187-INSERM U1196, F-91405 Orsay, France
| | - David Monchaud
- Institute of Molecular Chemistry, University of Dijon, ICMUB CNRS UMR6302, F-21078 Dijon, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, CNRS UMR9187-INSERM U1196, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, UMR9187-INSERM U1196, F-91405 Orsay, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, F-91405 Orsay, France; Equipe Labellisée Ligue Contre le Cancer, F-91405 Orsay, France.
| |
Collapse
|
36
|
Bukhari SIA, Vasudevan S. FXR1a-associated microRNP: A driver of specialized non-canonical translation in quiescent conditions. RNA Biol 2016; 14:137-145. [PMID: 27911187 DOI: 10.1080/15476286.2016.1265197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Eukaryotic protein synthesis is a multifaceted process that requires coordination of a set of translation factors in a particular cellular state. During normal growth and proliferation, cells generally make their proteome via conventional translation that utilizes canonical translation factors. When faced with environmental stress such as growth factor deprivation, or in response to biological cues such as developmental signals, cells can reduce canonical translation. In this situation, cells adapt alternative modes of translation to make specific proteins necessary for required biological functions under these distinct conditions. To date, a number of alternative translation mechanisms have been reported, which include non-canonical, cap dependent translation and cap independent translation such as IRES mediated translation. Here, we discuss one of the alternative modes of translation mediated by a specialized microRNA complex, FXR1a-microRNP that promotes non-canonical, cap dependent translation in quiescent conditions, where canonical translation is reduced due to low mTOR activity.
Collapse
Affiliation(s)
- Syed I A Bukhari
- a Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - Shobha Vasudevan
- a Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| |
Collapse
|
37
|
Ahuja D, Goyal A, Ray PS. Interplay between RNA-binding protein HuR and microRNA-125b regulates p53 mRNA translation in response to genotoxic stress. RNA Biol 2016; 13:1152-1165. [PMID: 27592685 PMCID: PMC5100343 DOI: 10.1080/15476286.2016.1229734] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Tumor suppressor protein p53 plays a crucial role in maintaining genomic integrity in response to DNA damage. Regulation of translation of p53 mRNA is a major mode of regulation of p53 expression under genotoxic stress. The AU/U-rich element-binding protein HuR has been shown to bind to p53 mRNA 3′UTR and enhance translation in response to DNA-damaging UVC radiation. On the other hand, the microRNA miR-125b is reported to repress p53 expression and stress-induced apoptosis. Here, we show that UVC radiation causes an increase in miR-125b level in a biphasic manner, as well as nuclear cytoplasmic translocation of HuR. Binding of HuR to the p53 mRNA 3′UTR, especially at a site adjacent to the miR-125b target site, causes dissociation of the p53 mRNA from the RNA-induced silencing complex (RISC) and inhibits the miR-125b-mediated translation repression of p53. HuR prevents the oncogenic effect of miR-125b by reversing the decrease in apoptosis and increase in cell proliferation caused by the overexpression of miR-125b. The antagonistic interplay between miR-125b and HuR might play an important role in fine-tuning p53 gene expression at the post-transcriptional level, and thereby regulate the cellular response to genotoxic stress.
Collapse
Affiliation(s)
- Deepika Ahuja
- a Department of Biological Sciences , Indian Institute of Science Education and Research , Kolkata, Mohanpur, Nadia , West Bengal , India
| | - Ashish Goyal
- a Department of Biological Sciences , Indian Institute of Science Education and Research , Kolkata, Mohanpur, Nadia , West Bengal , India
| | - Partho Sarothi Ray
- a Department of Biological Sciences , Indian Institute of Science Education and Research , Kolkata, Mohanpur, Nadia , West Bengal , India
| |
Collapse
|
38
|
Anastasakis D, Skeparnias I, Shaukat AN, Grafanaki K, Kanellou A, Taraviras S, Papachristou DJ, Papakyriakou A, Stathopoulos C. Mammalian PNLDC1 is a novel poly(A) specific exonuclease with discrete expression during early development. Nucleic Acids Res 2016; 44:8908-8920. [PMID: 27515512 PMCID: PMC5062988 DOI: 10.1093/nar/gkw709] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/02/2016] [Indexed: 12/28/2022] Open
Abstract
PNLDC1 is a homologue of poly(A) specific ribonuclease (PARN), a known deadenylase with additional role in processing of non-coding RNAs. Both enzymes were reported recently to participate in piRNA biogenesis in silkworm and C. elegans, respectively. To get insights on the role of mammalian PNLDC1, we characterized the human and mouse enzymes. PNLDC1 shows limited conservation compared to PARN and represents an evolutionary related but distinct group of enzymes. It is expressed specifically in mouse embryonic stem cells, human and mouse testes and during early mouse embryo development, while it fades during differentiation. Its expression in differentiated cells, is suppressed through methylation of its promoter by the de novo methyltransferase DNMT3B. Both enzymes are localized mainly in the ER and exhibit in vitro specificity restricted solely to 3′ RNA or DNA polyadenylates. Knockdown of Pnldc1 in mESCs and subsequent NGS analysis showed that although the expression of the remaining deadenylases remains unaffected, it affects genes involved mainly in reprogramming, cell cycle and translational regulation. Mammalian PNLDC1 is a novel deadenylase expressed specifically in cell types which share regulatory mechanisms required for multipotency maintenance. Moreover, it could be involved both in posttranscriptional regulation through deadenylation and genome surveillance during early development.
Collapse
Affiliation(s)
- Dimitrios Anastasakis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | | | - Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Alexandra Kanellou
- Department of Physiology, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Dionysios J Papachristou
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Patras, 26504 Rio Achaia, Greece
| | - Athanasios Papakyriakou
- Laboratory of Chemical Biology, National Centre for Scientific Research 'Demokritos', 15341 Athens, Greece
| | | |
Collapse
|
39
|
Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA. Cell Discov 2016; 2:16013. [PMID: 27462460 PMCID: PMC4906801 DOI: 10.1038/celldisc.2016.13] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
The DNA damage response involves coordinated control of gene expression and DNA repair. Using deep sequencing, we found widespread changes of alternative cleavage and polyadenylation site usage on ultraviolet-treatment in mammalian cells. Alternative cleavage and polyadenylation regulation in the 3ʹ untranslated region is substantial, leading to both shortening and lengthening of 3ʹ untranslated regions of genes. Interestingly, a strong activation of intronic alternative cleavage and polyadenylation sites is detected, resulting in widespread expression of truncated transcripts. Intronic alternative cleavage and polyadenylation events are biased to the 5ʹ end of genes and affect gene groups with important functions in DNA damage response and cancer. Moreover, intronic alternative cleavage and polyadenylation site activation during DNA damage response correlates with a decrease in U1 snRNA levels, and is reversible by U1 snRNA overexpression. Importantly, U1 snRNA overexpression mitigates ultraviolet-induced apoptosis. Together, these data reveal a significant gene regulatory scheme in DNA damage response where U1 snRNA impacts gene expression via the U1-alternative cleavage and polyadenylation axis.
Collapse
|