1
|
Xiong C, Sun Z, Yu J, Lin Y. Exosome Component 4 Promotes Epithelial Ovarian Cancer Cell Proliferation, Migration, and Invasion via the Wnt Pathway. Front Oncol 2021; 11:797968. [PMID: 34956910 PMCID: PMC8692763 DOI: 10.3389/fonc.2021.797968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
Background Of gynecologic malignancies, ovarian cancer is the leading cause of death, mainly due to the lack of sensitive tumor markers, which means it almost always presents at an advanced stage. Exosome Component 4 (EXOSC4) is involved in RNA degradation, but its role in epithelial ovarian cancer (EOC) is unclear. Methods The expression levels of EXOSC4 in EOC and normal ovarian tissue specimens were determined by immunohistochemical staining. The overall survival (OS) and progression-free survival (PFS) of patients with EOC were evaluated after patients were classified into high and low EXOSC4 expression groups, and the Cox regression model was established to identify independent predictors of patient prognosis. The effects of EXOSC4 on proliferation, colony formation, migration, and invasion were examined in the SKOV-3 and HO8910 cell lines by lentivirus-mediated shRNA knockdown. Flow cytometry was used to detect cell cycle changes. The mRNA levels of cyclin D1, CDK4, and c-myc were detected by RT-PCR. The protein expression levels of β-catenin, cyclin D1, CDK4, c-myc, vimentin, N-cadherin, and E-cadherin were assessed by western blot. Wnt/β-catenin activation was measured by TCF/LEF reporter assay. Results EXOSC4 was significantly elevated in EOC tissues and cell lines. High EXOSC4 expression was correlated with the International Federation of Gynecology and Obstetrics (FIGO) stage and pathological grade, and identified as an independent predictor of shorter OS and PFS. EXOSC4 knockdown suppressed proliferation, migration, and invasion in EOC cell lines. Cells were arrested at G0/G1 phase after EXOSC4 knockdown. The mRNA levels of cyclin D1, CDK4, and c-myc were decreased. β-catenin, cyclin D1, CDK4, c-myc, vimentin, and N-cadherin protein expression levels were reduced, while those of E-cadherin was increased. Wnt/β-catenin activity was suppressed after the EXOSC4 knockdown. Conclusions EXOSC4 is involved in EOC. Knockdown of EXOSC4 can inhibit the proliferation, migration, and invasion ability of EOC by suppressing the Wnt pathway. EXOSC4 is expected to be a novel biomarker and molecular target in EOC.
Collapse
Affiliation(s)
- Chang Xiong
- Department of Obstetrics and Gynecology, Affiliated Hospital of Jiangnan University, Wuxi, China.,Wuxi Medical College, Jiangnan University, Wuxi, China
| | - Zhongfeng Sun
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Jinjin Yu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Jiangnan University, Wuxi, China.,Wuxi Medical College, Jiangnan University, Wuxi, China
| | - Yaying Lin
- Department of Obstetrics and Gynecology, Affiliated Hospital of Jiangnan University, Wuxi, China.,Wuxi Medical College, Jiangnan University, Wuxi, China
| |
Collapse
|
2
|
Noncoding RNA Roles in Pharmacogenomic Responses to Aspirin: New Molecular Mechanisms for an Old Drug. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6830560. [PMID: 34926688 PMCID: PMC8677408 DOI: 10.1155/2021/6830560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022]
Abstract
Aspirin, as one of the most frequently prescribed drugs, can have therapeutic effects on different conditions such as cardiovascular and metabolic disorders and malignancies. The effects of this common cardiovascular drug are exerted through different molecular and cellular pathways. Altered noncoding RNA (ncRNA) expression profiles during aspirin treatments indicate a close relationship between these regulatory molecules and aspirin effects through regulating gene expressions. A better understanding of the molecular networks contributing to aspirin efficacy would help optimize efficient therapies for this very popular drug. This review is aimed at discussing and highlighting the identified interactions between aspirin and ncRNAs and their targeting pathways and better understanding pharmacogenetic responses to aspirin.
Collapse
|
3
|
|
4
|
Tatullo M, Marrelli B, Zullo MJ, Codispoti B, Paduano F, Benincasa C, Fortunato F, Scacco S, Zavan B, Cocco T. Exosomes from Human Periapical Cyst-MSCs: Theranostic Application in Parkinson's Disease. Int J Med Sci 2020; 17:657-663. [PMID: 32210716 PMCID: PMC7085217 DOI: 10.7150/ijms.41515] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/08/2020] [Indexed: 12/17/2022] Open
Abstract
The scientific community continuously strives to get new disease models, to discover early markers or novel therapeutic approaches, improving the diagnosis and prognosis of several human pathologies. Parkinson's Disease (PD) is characterized by a long asymptomatic phase, characterized by a selective loss of dopaminergic neurons. Recently, the human Periapical Cyst-Mesenchymal Stem Cells (hPCy-MSCs) have been differentiated in functional dopaminergic neurons: such oral-derived MSCs and the hPCy-MSCs-derived exosomes may represent a strategic and useful in vitro study-model, as well as intriguing therapeutic carriers. Circadian rhythm (CR) alteration variously impacts on PD pathways: an interesting research target is represented by the analysis of the exosomes released by dopaminergic neurons, derived from neural-differentiated hPCy-MSCs, after having reproduced in-vitro PD-like conditions. This review aims to describe the crosstalk among some aspects of circadian rhythm related to the onset of PD and the exosomes released by cells of PD patients. More in detail: the first part of this article will describe the main characteristics of circadian rhythm and the involvement of the exosomes found to be effective in the pathogenesis of PD. Finally, the authors will suggest how those exosomes derived from dopaminergic neurons, obtained by oral-derived stem cells (hPCy-MSCs) may represent a smart model for the in vitro research on PD, to find new biomarkers, to test new drugs or, fatally, to find new pathways applicable in future therapeutic approaches.
Collapse
Affiliation(s)
- Marco Tatullo
- Marrelli Health - Tecnologica Research Institute, Biomedical Section, Street E. Fermi, Crotone, Italy
- Department of Therapeutic Dentistry, Sechenov University Russia, Moscow, Russia
| | - Benedetta Marrelli
- Marrelli Health - Tecnologica Research Institute, Biomedical Section, Street E. Fermi, Crotone, Italy
- Department of Therapeutic Dentistry, Sechenov University Russia, Moscow, Russia
| | - Maria Josephine Zullo
- Department of Internal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Bruna Codispoti
- Marrelli Health - Tecnologica Research Institute, Biomedical Section, Street E. Fermi, Crotone, Italy
| | - Francesco Paduano
- Marrelli Health - Tecnologica Research Institute, Biomedical Section, Street E. Fermi, Crotone, Italy
| | - Caterina Benincasa
- Marrelli Health - Tecnologica Research Institute, Biomedical Section, Street E. Fermi, Crotone, Italy
| | - Francesco Fortunato
- Department of Neurological Sciences, University of Catanzaro “Magna Graecia”, Italy
| | - Salvatore Scacco
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari “Aldo Moro”, Italy
| | - Barbara Zavan
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Tiziana Cocco
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari “Aldo Moro”, Italy
| |
Collapse
|
5
|
McIver SC, Katsumura KR, Davids E, Liu P, Kang YA, Yang D, Bresnick EH. Exosome complex orchestrates developmental signaling to balance proliferation and differentiation during erythropoiesis. eLife 2016; 5. [PMID: 27543448 PMCID: PMC5040589 DOI: 10.7554/elife.17877] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/18/2016] [Indexed: 12/11/2022] Open
Abstract
Since the highly conserved exosome complex mediates the degradation and processing of multiple classes of RNAs, it almost certainly controls diverse biological processes. How this post-transcriptional RNA-regulatory machine impacts cell fate decisions and differentiation is poorly understood. Previously, we demonstrated that exosome complex subunits confer an erythroid maturation barricade, and the erythroid transcription factor GATA-1 dismantles the barricade by transcriptionally repressing the cognate genes. While dissecting requirements for the maturation barricade in Mus musculus, we discovered that the exosome complex is a vital determinant of a developmental signaling transition that dictates proliferation/amplification versus differentiation. Exosome complex integrity in erythroid precursor cells ensures Kit receptor tyrosine kinase expression and stem cell factor/Kit signaling, while preventing responsiveness to erythropoietin-instigated signals that promote differentiation. Functioning as a gatekeeper of this developmental signaling transition, the exosome complex controls the massive production of erythroid cells that ensures organismal survival in homeostatic and stress contexts. DOI:http://dx.doi.org/10.7554/eLife.17877.001 Red blood cells supply an animal’s tissues with the oxygen they need to survive. These cells circulate for a certain amount of time before they die. To replenish the red blood cells that are lost, first a protein called stem cell factor (SCF) instructs stem cells and precursor cells to proliferate, and a second protein, known as erythropoietin, then signals to these cells to differentiate into mature red blood cells. It is important to maintain this balance between these two processes because too much proliferation can lead to cancer while too much differentiation will exhaust the supply of stem cells. Previous work has shown that a collection of proteins called the exosome complex can block steps leading towards mature red blood cells. The exosome complex controls several processes within cells by modifying or degrading a variety of messenger RNAs, the molecules that serve as intermediates between DNA and protein. However, it was not clear how the exosome complex sets up the differentiation block and whether it is somehow connected to the signaling from SCF and erythropoietin. McIver et al. set out to address this issue by isolating precursor cells with the potential to become red blood cells from mouse fetal livers and experimentally reducing the levels of the exosome complex. The experiments showed that these cells were no longer able to respond when treated with SCF in culture, whereas the control cells responded as normal. Further experiments showed that cells with less of the exosome complex also made less of a protein named Kit. Normally, SCF interacts with Kit to instruct cells to multiply. Lastly, although the experimental cells could no longer respond to these proliferation signals, they could react to erythropoietin, which promotes differentiation. Thus, normal levels of the exosome complex keep the delicate balance between proliferation and differentiation, which is crucial to the development of red blood cells. In future, it will be important to study the exosome complex in living mice and in human cells, and to see whether it also controls other signaling pathways. Furthermore, it is worth exploring whether this new knowledge can help efforts to produce red blood cells on an industrial scale, which could then be used to treat patients with conditions such as anemia. DOI:http://dx.doi.org/10.7554/eLife.17877.002
Collapse
Affiliation(s)
- Skye C McIver
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, United States.,UW-Madison Blood Research Program, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Koichi R Katsumura
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, United States.,UW-Madison Blood Research Program, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Elsa Davids
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, United States.,UW-Madison Blood Research Program, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Peng Liu
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Yoon-A Kang
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, United States.,UW-Madison Blood Research Program, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - David Yang
- Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, United States.,UW-Madison Blood Research Program, University of Wisconsin School of Medicine and Public Health, Madison, United States.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, United States
| |
Collapse
|
6
|
Liu L, Chen X. RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants. MOLECULAR PLANT 2016; 9:826-36. [PMID: 27045817 PMCID: PMC5123867 DOI: 10.1016/j.molp.2016.03.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 05/19/2023]
Abstract
RNA quality control of endogenous RNAs is an integral part of eukaryotic gene expression and often relies on exonucleolytic degradation to eliminate dysfunctional transcripts. In parallel, exogenous and selected endogenous RNAs are degraded through RNA silencing, which is a genome defense mechanism used by many eukaryotes. In plants, RNA silencing is triggered by the production of double-stranded RNAs (dsRNAs) by RNA-DEPENDENT RNA POLYMERASEs (RDRs) and proceeds through small interfering (si) RNA-directed, ARGONAUTE (AGO)-mediated cleavage of homologous transcripts. Many studies revealed that plants avert inappropriate posttranscriptional gene silencing of endogenous coding genes by using RNA surveillance mechanisms as a safeguard to protect their transcriptome profiles. The tug of war between RNA surveillance and RNA silencing ensures the appropriate partitioning of endogenous RNA substrates among these degradation pathways. Here we review recent advances on RNA quality control and its role in the suppression of RNA silencing at endogenous genes and discuss the mechanisms underlying the crosstalk among these pathways.
Collapse
Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA.
| |
Collapse
|
7
|
Rigo F, Seth PP, Bennett CF. Antisense oligonucleotide-based therapies for diseases caused by pre-mRNA processing defects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:303-52. [PMID: 25201110 DOI: 10.1007/978-1-4939-1221-6_9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Before a messenger RNA (mRNA) is translated into a protein in the cytoplasm, its pre-mRNA precursor is extensively processed through capping, splicing and polyadenylation in the nucleus. Defects in the processing of pre-mRNAs due to mutations in RNA sequences often cause disease. Traditional small molecules or protein-based therapeutics are not well suited for correcting processing defects by targeting RNA. However, antisense oligonucleotides (ASOs) designed to bind RNA by Watson-Crick base pairing can target most RNA transcripts and have emerged as the ideal therapeutic agents for diseases that are caused by pre-mRNA processing defects. Here we review the diverse ASO-based mechanisms that can be exploited to modulate the expression of RNA. We also discuss how advancements in medicinal chemistry and a deeper understanding of the pharmacokinetic and toxicological properties of ASOs have enabled their use as therapeutic agents. We end by describing how ASOs have been used successfully to treat various pre-mRNA processing diseases in animal models.
Collapse
Affiliation(s)
- Frank Rigo
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA, USA,
| | | | | |
Collapse
|
8
|
Portal MM, Pavet V, Erb C, Gronemeyer H. Human cells contain natural double-stranded RNAs with potential regulatory functions. Nat Struct Mol Biol 2014; 22:89-97. [PMID: 25504323 DOI: 10.1038/nsmb.2934] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/14/2014] [Indexed: 12/28/2022]
Abstract
Recent evidence has suggested the existence of sense-antisense transcription in mammals, but the existence of double-stranded RNAs endowed with biological function has remained elusive. Herein we show that hundreds of putative natural double-stranded RNAs (ndsRNAs) are expressed from interspersed genomic locations and respond to cellular cues. We demonstrate that a subset of ndsRNAs localize in the nucleus and, in their double-stranded form, interact with nuclear proteins. Detailed characterization of an ndsRNA (nds-2a) revealed that this molecule displays differential localization throughout the cell cycle and directly interacts with RCC1 and RAN and, through the latter, with the mitotic RANGAP1-SUMO1-RANBP2 complex. Notably, altering nds-2a levels led to postmitotic abnormalities, mitotic catastrophe and cell death, thus supporting a mitosis-related role. Altogether, our study reveals a hitherto-unrecognized class of RNAs that potentially participate in major biological processes in human cells.
Collapse
Affiliation(s)
- Maximiliano M Portal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Equipe Labellisée Ligue Contre le Cancer, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France
| | - Valeria Pavet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Equipe Labellisée Ligue Contre le Cancer, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France
| | - Cathie Erb
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Equipe Labellisée Ligue Contre le Cancer, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France
| | - Hinrich Gronemeyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Equipe Labellisée Ligue Contre le Cancer, Centre National de la Recherche Scientifique UMR 7104, Institut National de la Santé et de la Recherche Médicale U964, University of Strasbourg, Illkirch, France
| |
Collapse
|
9
|
McIver SC, Kang YA, DeVilbiss AW, O'Driscoll CA, Ouellette JN, Pope NJ, Camprecios G, Chang CJ, Yang D, Bouhassira EE, Ghaffari S, Bresnick EH. The exosome complex establishes a barricade to erythroid maturation. Blood 2014; 124:2285-97. [PMID: 25115889 PMCID: PMC4183988 DOI: 10.1182/blood-2014-04-571083] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/25/2014] [Indexed: 12/28/2022] Open
Abstract
Complex genetic networks control hematopoietic stem cell differentiation into progenitors that give rise to billions of erythrocytes daily. Previously, we described a role for the master regulator of erythropoiesis, GATA-1, in inducing genes encoding components of the autophagy machinery. In this context, the Forkhead transcription factor, Foxo3, amplified GATA-1-mediated transcriptional activation. To determine the scope of the GATA-1/Foxo3 cooperativity, and to develop functional insights, we analyzed the GATA-1/Foxo3-dependent transcriptome in erythroid cells. GATA-1/Foxo3 repressed expression of Exosc8, a pivotal component of the exosome complex, which mediates RNA surveillance and epigenetic regulation. Strikingly, downregulating Exosc8, or additional exosome complex components, in primary erythroid precursor cells induced erythroid cell maturation. Our results demonstrate a new mode of controlling erythropoiesis in which multiple components of the exosome complex are endogenous suppressors of the erythroid developmental program.
Collapse
Affiliation(s)
- Skye C McIver
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Yoon-A Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Andrew W DeVilbiss
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Chelsea A O'Driscoll
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Jonathan N Ouellette
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Nathaniel J Pope
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Genis Camprecios
- Department of Developmental and Regenerative Biology, Mt. Sinai School of Medicine, New York, NY
| | - Chan-Jung Chang
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY; and
| | - David Yang
- Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison WI
| | - Eric E Bouhassira
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY; and
| | - Saghi Ghaffari
- Department of Developmental and Regenerative Biology, Mt. Sinai School of Medicine, New York, NY
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| |
Collapse
|
10
|
Shin JH, Chekanova JA. Arabidopsis RRP6L1 and RRP6L2 function in FLOWERING LOCUS C silencing via regulation of antisense RNA synthesis. PLoS Genet 2014; 10:e1004612. [PMID: 25211139 PMCID: PMC4161302 DOI: 10.1371/journal.pgen.1004612] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/18/2014] [Indexed: 01/24/2023] Open
Abstract
The exosome complex functions in RNA metabolism and transcriptional gene silencing. Here, we report that mutations of two Arabidopsis genes encoding nuclear exosome components AtRRP6L1 and AtRRP6L2, cause de-repression of the main flowering repressor FLOWERING LOCUS C (FLC) and thus delay flowering in early-flowering Arabidopsis ecotypes. AtRRP6L mutations affect the expression of known FLC regulatory antisense (AS) RNAs AS I and II, and cause an increase in Histone3 K4 trimethylation (H3K4me3) at FLC. AtRRP6L1 and AtRRP6L2 function redundantly in regulation of FLC and also act independently of the exosome core complex. Moreover, we discovered a novel, long non-coding, non-polyadenylated antisense transcript (ASL, for Antisense Long) originating from the FLC locus in wild type plants. The AtRRP6L proteins function as the main regulators of ASL synthesis, as these mutants show little or no ASL transcript. Unlike ASI/II, ASL associates with H3K27me3 regions of FLC, suggesting that it could function in the maintenance of H3K27 trimethylation during vegetative growth. AtRRP6L mutations also affect H3K27me3 levels and nucleosome density at the FLC locus. Furthermore, AtRRP6L1 physically associates with the ASL transcript and directly interacts with the FLC locus. We propose that AtRRP6L proteins participate in the maintenance of H3K27me3 at FLC via regulating ASL. Furthermore, AtRRP6Ls might participate in multiple FLC silencing pathways by regulating diverse antisense RNAs derived from the FLC locus.
Collapse
Affiliation(s)
- Jun-Hye Shin
- School of Biological Sciences, University of Missouri - Kansas City, Kansas City, Missouri, United States of America
| | - Julia A. Chekanova
- School of Biological Sciences, University of Missouri - Kansas City, Kansas City, Missouri, United States of America
- * E-mail:
| |
Collapse
|
11
|
Mansoori B, Sandoghchian Shotorbani S, Baradaran B. RNA interference and its role in cancer therapy. Adv Pharm Bull 2014; 4:313-21. [PMID: 25436185 DOI: 10.5681/apb.2014.046] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/16/2014] [Accepted: 04/19/2014] [Indexed: 12/21/2022] Open
Abstract
In todays' environment, it is becoming increasingly difficult to ignore the role of cancer in social health. Although a huge budget is allocated on cancer research every year, cancer remains the second global cause of death. And, exclusively, less than 50% of patients afflicted with advanced cancer live one year subsequent to standard cancer treatments. RNA interference (RNAi) is a mechanism for gene silencing. Such mechanism possesses uncanny ability in targeting cancer-related genes. A majority of gene products involved in tumorigenesis have recently been utilized as targets in RNAi based therapy. The evidence from these studies indicates that RNAi application for targeting functional carcinogenic molecules, tumor resistance to chemotherapy and radiotherapy is required in today's cancer treatment. Knock downing of gene products by RNAi technology exerts antiproliferative and proapoptotic effects upon cell culture systems, animal models and in clinical trials in the most studies. The recognition of RNAi mechanism and the progress in this field leaded several new RNAi-based drugs to Clinical Trial phases. This has also developed genome based personalized cancer therapeutics. Hopefully, this type of treatment will work as one of the efficient one for cancer patients.
Collapse
Affiliation(s)
- Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
12
|
Quality control of mRNP biogenesis: networking at the transcription site. Semin Cell Dev Biol 2014; 32:37-46. [PMID: 24713468 DOI: 10.1016/j.semcdb.2014.03.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 03/28/2014] [Indexed: 11/20/2022]
Abstract
Eukaryotic cells carry out quality control (QC) over the processes of RNA biogenesis to inactivate or eliminate defective transcripts, and to avoid their production. In the case of protein-coding transcripts, the quality controls can sense defects in the assembly of mRNA-protein complexes, in the processing of the precursor mRNAs, and in the sequence of open reading frames. Different types of defect are monitored by different specialized mechanisms. Some of them involve dedicated factors whose function is to identify faulty molecules and target them for degradation. Others are the result of a more subtle balance in the kinetics of opposing activities in the mRNA biogenesis pathway. One way or another, all such mechanisms hinder the expression of the defective mRNAs through processes as diverse as rapid degradation, nuclear retention and transcriptional silencing. Three major degradation systems are responsible for the destruction of the defective transcripts: the exosome, the 5'-3' exoribonucleases, and the nonsense-mediated mRNA decay (NMD) machinery. This review summarizes recent findings on the cotranscriptional quality control of mRNA biogenesis, and speculates that a protein-protein interaction network integrates multiple mRNA degradation systems with the transcription machinery.
Collapse
|
13
|
Kumakura N, Otsuki H, Tsuzuki M, Takeda A, Watanabe Y. Arabidopsis AtRRP44A is the functional homolog of Rrp44/Dis3, an exosome component, is essential for viability and is required for RNA processing and degradation. PLoS One 2013; 8:e79219. [PMID: 24244451 PMCID: PMC3820695 DOI: 10.1371/journal.pone.0079219] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 09/26/2013] [Indexed: 11/25/2022] Open
Abstract
The RNA exosome is a multi-subunit complex that is responsible for 3ʹ to 5ʹ degradation and processing of cellular RNA. Rrp44/Dis3 is the catalytic center of the exosome in yeast and humans. However, the role of Rrp44/Dis3 homologs in plants is still unidentified. Here, we show that Arabidopsis AtRRP44A is the functional homolog of Rrp44/Dis3, is essential for plant viability and is required for RNA processing and degradation. We characterized AtRRP44A and AtRRP44B/SOV, two predicted Arabidopsis Rrp44/Dis3 homologs. AtRRP44A could functionally replace S. cerevisiae Rrp44/Dis3, but AtRRP44B/SOV could not. rrp44a knock-down mutants showed typical phenotypes of exosome function deficiency, 5.8S rRNA 3ʹ extension and rRNA maturation by-product over-accumulation, but rrp44b mutants did not. Conversely, AtRRP44B/SOV mutants showed elevated levels of a selected mRNA, on which rrp44a did not have detectable effects. Although T-DNA insertion mutants of AtRRP44B/SOV had no obvious phenotype, those of AtRRP44A showed defects in female gametophyte development and early embryogenesis. These results indicate that AtRRP44A and AtRRP44B/SOV have independent roles for RNA turnover in plants.
Collapse
Affiliation(s)
- Naoyoshi Kumakura
- Department of Life Sciences, Graduate School of Arts and Sciences, the University of Tokyo, Tokyo, Japan
| | | | | | | | | |
Collapse
|
14
|
Feigenbutz M, Jones R, Besong TMD, Harding SE, Mitchell P. Assembly of the yeast exoribonuclease Rrp6 with its associated cofactor Rrp47 occurs in the nucleus and is critical for the controlled expression of Rrp47. J Biol Chem 2013; 288:15959-70. [PMID: 23580640 PMCID: PMC3668751 DOI: 10.1074/jbc.m112.445759] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Rrp6 is a key catalytic subunit of the nuclear RNA exosome that plays a pivotal role in the processing, degradation, and quality control of a wide range of cellular RNAs. Here we report our findings on the assembly of the complex involving Rrp6 and its associated protein Rrp47, which is required for many Rrp6-mediated RNA processes. Recombinant Rrp47 is expressed as a non-globular homodimer. Analysis of the purified recombinant Rrp6·Rrp47 complex revealed a heterodimer, suggesting that Rrp47 undergoes a structural reconfiguration upon interaction with Rrp6. Studies using GFP fusion proteins show that Rrp6 and Rrp47 are localized to the yeast cell nucleus independently of one another. Consistent with this data, Rrp6, but not Rrp47, is found associated with the nuclear import adaptor protein Srp1. We show that the interaction with Rrp6 is critical for Rrp47 stability in vivo; in the absence of Rrp6, newly synthesized Rrp47 is rapidly degraded in a proteasome-dependent manner. These data resolve independent nuclear import routes for Rrp6 and Rrp47, reveal a structural reorganization of Rrp47 upon its interaction with Rrp6, and demonstrate a proteasome-dependent mechanism that efficiently suppresses the expression of Rrp47 in the absence of Rrp6.
Collapse
Affiliation(s)
- Monika Feigenbutz
- Molecular Biology and Biotechnology Department, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | | | | | | | | |
Collapse
|
15
|
Shin JH, Wang HLV, Lee J, Dinwiddie BL, Belostotsky DA, Chekanova JA. The role of the Arabidopsis Exosome in siRNA-independent silencing of heterochromatic loci. PLoS Genet 2013; 9:e1003411. [PMID: 23555312 PMCID: PMC3610620 DOI: 10.1371/journal.pgen.1003411] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 02/11/2013] [Indexed: 01/08/2023] Open
Abstract
The exosome functions throughout eukaryotic RNA metabolism and has a prominent role in gene silencing in yeast. In Arabidopsis, exosome regulates expression of a "hidden" transcriptome layer from centromeric, pericentromeric, and other heterochromatic loci that are also controlled by small (sm)RNA-based de novo DNA methylation (RdDM). However, the relationship between exosome and smRNAs in gene silencing in Arabidopsis remains unexplored. To investigate whether exosome interacts with RdDM, we profiled Arabidopsis smRNAs by deep sequencing in exosome and RdDM mutants and also analyzed RdDM-controlled loci. We found that exosome loss had a very minor effect on global smRNA populations, suggesting that, in contrast to fission yeast, in Arabidopsis the exosome does not control the spurious entry of RNAs into smRNA pathways. Exosome defects resulted in decreased histone H3K9 dimethylation at RdDM-controlled loci, without affecting smRNAs or DNA methylation. Exosome also exhibits a strong genetic interaction with RNA Pol V, but not Pol IV, and physically associates with transcripts produced from the scaffold RNAs generating region. We also show that two Arabidopsis rrp6 homologues act in gene silencing. Our data suggest that Arabidopsis exosome may act in parallel with RdDM in gene silencing, by epigenetic effects on chromatin structure, not through siRNAs or DNA methylation.
Collapse
Affiliation(s)
- Jun-Hye Shin
- School of Biological Sciences, University of Missouri–Kansas City, Kansas City, Missouri, United States of America
| | - Hsiao-Lin V. Wang
- School of Biological Sciences, University of Missouri–Kansas City, Kansas City, Missouri, United States of America
| | - Jinwon Lee
- School of Biological Sciences, University of Missouri–Kansas City, Kansas City, Missouri, United States of America
| | - Brandon L. Dinwiddie
- School of Biological Sciences, University of Missouri–Kansas City, Kansas City, Missouri, United States of America
| | - Dmitry A. Belostotsky
- School of Biological Sciences, University of Missouri–Kansas City, Kansas City, Missouri, United States of America
| | - Julia A. Chekanova
- School of Biological Sciences, University of Missouri–Kansas City, Kansas City, Missouri, United States of America
- * E-mail:
| |
Collapse
|
16
|
Mistry DS, Chen Y, Sen GL. Progenitor function in self-renewing human epidermis is maintained by the exosome. Cell Stem Cell 2012; 11:127-35. [PMID: 22770246 DOI: 10.1016/j.stem.2012.04.022] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 03/22/2012] [Accepted: 04/24/2012] [Indexed: 01/25/2023]
Abstract
Stem and progenitor cells maintain the tissue they reside in for life by regulating the balance between proliferation and differentiation. How this is done is not well understood. Here, we report that the human exosome maintains progenitor cell function. The expression of several subunits of the exosome were found to be enriched in epidermal progenitor cells, which were required to retain proliferative capacity and to prevent premature differentiation. Loss of PM/Scl-75 also known as EXOSC9, a key subunit of the exosome complex, resulted in loss of cells from the progenitor cell compartment, premature differentiation, and loss of epidermal tissue. EXOSC9 promotes self-renewal and prevents premature differentiation by maintaining transcript levels of a transcription factor necessary for epidermal differentiation, GRHL3, at low levels through mRNA degradation. These data demonstrate that control of differentiation specific transcription factors through mRNA degradation is required for progenitor cell maintenance in mammalian tissue.
Collapse
Affiliation(s)
- Devendra S Mistry
- Division of Dermatology, Department of Medicine, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | | | | |
Collapse
|
17
|
Plant Exosomes and Cofactors. EUKARYOTIC RNASES AND THEIR PARTNERS IN RNA DEGRADATION AND BIOGENESIS, PART A 2012; 31:31-52. [DOI: 10.1016/b978-0-12-404740-2.00002-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
18
|
Christie M, Brosnan CA, Rothnagel JA, Carroll BJ. RNA decay and RNA silencing in plants: competition or collaboration? FRONTIERS IN PLANT SCIENCE 2011; 2:99. [PMID: 22639621 PMCID: PMC3355627 DOI: 10.3389/fpls.2011.00099] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 11/30/2011] [Indexed: 05/25/2023]
Abstract
Initiation of RNA polymerase II transcription signals the beginning of a series of physically and functionally coupled pre-mRNA processing events that transform an RNA transcript into a highly structured, mature ribonucleoprotein complex. With such a complexity of co-transcriptional processes comes the need to identify and degrade improperly processed transcripts. Quality control of mRNA expression primarily involves exonucleolytic degradation of aberrant RNAs. RNA silencing, on the other hand, tends to be viewed separately as a pathway that primarily functions in regulating endogenous gene expression and in genome defense against transposons and viruses. Here, we review current knowledge of these pathways as they exist in plants and draw parallels to similar pathways in other eukaryotes. We then highlight some unexplored overlaps that exist between the RNA silencing and RNA decay pathways of plants, as evidenced by their shared RNA substrates and shared genetic requirements.
Collapse
Affiliation(s)
- Michael Christie
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia
| | - Christopher A. Brosnan
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia
| | - Joseph A. Rothnagel
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia
| |
Collapse
|
19
|
Williams CW, Elmendorf HG. Identification and analysis of the RNA degrading complexes and machinery of Giardia lamblia using an in silico approach. BMC Genomics 2011; 12:586. [PMID: 22126454 PMCID: PMC3282835 DOI: 10.1186/1471-2164-12-586] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 11/29/2011] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND RNA degradation is critical to the survival of all cells. With increasing evidence for pervasive transcription in cells, RNA degradation has gained recognition as a means of regulating gene expression. Yet, RNA degradation machinery has been studied extensively in only a few eukaryotic organisms, including Saccharomyces cerevisiae and humans. Giardia lamblia is a parasitic protist with unusual genomic traits: it is binucleated and tetraploid, has a very compact genome, displays a theme of genomic minimalism with cellular machinery commonly comprised of a reduced number of protein components, and has a remarkably large population of long, stable, noncoding, antisense RNAs. RESULTS Here we use in silico approaches to investigate the major RNA degradation machinery in Giardia lamblia and compare it to a broad array of other parasitic protists. We have found key constituents of the deadenylation and decapping machinery and of the 5'-3' RNA degradation pathway. We have similarly found that all of the major 3'-5' RNA degradation pathways are present in Giardia, including both exosome-dependent and exosome-independent machinery. However, we observe significant loss of RNA degradation machinery genes that will result in important differences in the protein composition, and potentially functionality, of the various RNA degradation pathways. This is most apparent in the exosome, the central mediator of 3'-5' degradation, which apparently contains an altered core configuration in both Giardia and Plasmodium, with only four, instead of the canonical six, distinct subunits. Additionally the exosome in Giardia is missing both the Rrp6, Nab3, and Nrd1 proteins, known to be key regulators of noncoding transcript stability in other cells. CONCLUSIONS These findings suggest that although the full complement of the major RNA degradation mechanisms were present - and likely functional - early in eukaryotic evolution, the composition and function of the complexes is more variable than previously appreciated. We suggest that the missing components of the exosome complex provide an explanation for the stable abundance of sterile RNA species in Giardia.
Collapse
Affiliation(s)
| | - Heidi G Elmendorf
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| |
Collapse
|
20
|
Kojima S, Shingle DL, Green CB. Post-transcriptional control of circadian rhythms. J Cell Sci 2011; 124:311-20. [PMID: 21242310 DOI: 10.1242/jcs.065771] [Citation(s) in RCA: 190] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Circadian rhythms exist in most living organisms. The general molecular mechanisms that are used to generate 24-hour rhythms are conserved among organisms, although the details vary. These core clocks consist of multiple regulatory feedback loops, and must be coordinated and orchestrated appropriately for the fine-tuning of the 24-hour period. Many levels of regulation are important for the proper functioning of the circadian clock, including transcriptional, post-transcriptional and post-translational mechanisms. In recent years, new information about post-transcriptional regulation in the circadian system has been discovered. Such regulation has been shown to alter the phase and amplitude of rhythmic mRNA and protein expression in many organisms. Therefore, this Commentary will provide an overview of current knowledge of post-transcriptional regulation of the clock genes and clock-controlled genes in dinoflagellates, plants, fungi and animals. This article will also highlight how circadian gene expression is modulated by post-transcriptional mechanisms and how this is crucial for robust circadian rhythmicity.
Collapse
Affiliation(s)
- Shihoko Kojima
- Department of Neuroscience, University of Texas Southwestern Medical Center, NB4.204G, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | | | | |
Collapse
|
21
|
Affiliation(s)
- Harm van Bakel
- Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Corey Nislow
- Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin J. Blencowe
- Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Timothy R. Hughes
- Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
22
|
Zimmer SL, McEvoy SM, Li J, Qu J, Read LK. A novel member of the RNase D exoribonuclease family functions in mitochondrial guide RNA metabolism in Trypanosoma brucei. J Biol Chem 2011; 286:10329-40. [PMID: 21252235 PMCID: PMC3060487 DOI: 10.1074/jbc.m110.152439] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 01/18/2011] [Indexed: 12/22/2022] Open
Abstract
RNA turnover and RNA editing are essential for regulation of mitochondrial gene expression in Trypanosoma brucei. RNA turnover is controlled in part by RNA 3' adenylation and uridylation status, with trans-acting factors also impacting RNA homeostasis. However, little is known about the mitochondrial degradation machinery or its regulation in T. brucei. We have identified a mitochondrial exoribonuclease, TbRND, whose expression is highly up-regulated in the insect proliferative stage of the parasite. TbRND shares sequence similarity with RNase D family enzymes but differs from all reported members of this family in possessing a CCHC zinc finger domain. In vitro, TbRND exhibits 3' to 5' exoribonuclease activity, with specificity toward uridine homopolymers, including the 3' oligo(U) tails of guide RNAs (gRNAs) that provide the sequence information for RNA editing. Several lines of evidence generated from RNAi-mediated knockdown and overexpression cell lines indicate that TbRND functions in gRNA metabolism in vivo. First, TbRND depletion results in gRNA tails extended by 2-3 nucleotides on average. Second, overexpression of wild type but not catalytically inactive TbRND results in a substantial decrease in the total gRNA population and a consequent inhibition of RNA editing. The observed effects on the gRNA population are specific as rRNAs, which are also 3'-uridylated, are unaffected by TbRND depletion or overexpression. Finally, we show that gRNA binding proteins co-purify with TbRND. In summary, TbRND is a novel 3' to 5' exoribonuclease that appears to have evolved a function highly specific to the mitochondrion of trypanosomes.
Collapse
Affiliation(s)
- Sara L. Zimmer
- From the Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214 and
| | - Sarah M. McEvoy
- From the Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214 and
| | - Jun Li
- the Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, New York 14260
| | - Jun Qu
- the Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, New York 14260
| | - Laurie K. Read
- From the Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14214 and
| |
Collapse
|
23
|
Qureshi IA, Mehler MF. Non-coding RNA networks underlying cognitive disorders across the lifespan. Trends Mol Med 2011; 17:337-46. [PMID: 21411369 DOI: 10.1016/j.molmed.2011.02.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 02/04/2011] [Accepted: 02/08/2011] [Indexed: 02/06/2023]
Abstract
Non-coding RNAs (ncRNAs) and their associated regulatory networks are increasingly being implicated in mediating a complex repertoire of neurobiological functions. Cognitive and behavioral processes are proving to be no exception. In this review, we discuss the emergence of many novel, diverse and rapidly expanding classes and subclasses of short and long ncRNAs. We briefly review the life cycles and molecular functions of these ncRNAs. We also examine how ncRNA circuitry mediates brain development, plasticity, stress responses and aging, and highlight its potential roles in the pathophysiology of cognitive disorders, including neural developmental and age-associated neurodegenerative diseases, as well as those that manifest throughout the lifespan.
Collapse
Affiliation(s)
- Irfan A Qureshi
- Rosyln and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
| | | |
Collapse
|
24
|
Bartoszewski R, Rab A, Fu L, Bartoszewska S, Collawn J, Bebok Z. CFTR expression regulation by the unfolded protein response. Methods Enzymol 2011; 491:3-24. [PMID: 21329791 DOI: 10.1016/b978-0-12-385928-0.00001-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel and key regulator of epithelial functions. Mutations in the CFTR gene lead to reduced or dysfunctional CFTR protein and cause cystic fibrosis (CF), a generalized exocrinopathy affecting multiple organs. In the airways, loss of CFTR function leads to thickened mucus, reduced mucociliary clearance, chronic infections, and respiratory failure. Common airway disorders such as bronchitis and chronic obstructive pulmonary disease (COPD) also present CF-like symptoms such as mucus congestion and chronic inflammation without mutations in CFTR. The primary risk factors for COPD and chronic bronchitis include environmental stress insults such as pollutants and infections that often result in hypoxic conditions. Furthermore, environmental factors such as cigarette smoke and reactive oxygen species have been implicated in reduced CFTR function. Activation of cellular stress responses by these factors promotes differential, stress-associated gene expression regulation. During our investigations on the mechanisms of CFTR expression regulation, we have shown that the ER stress response, the unfolded protein response (UPR), decreases CFTR expression at the transcriptional, translational, and maturational levels. Here, we provide a detailed description of the methods we employ to study CFTR expression regulation by the UPR. Similar approaches are applicable in studies on other genes and how they are affected by the UPR.
Collapse
Affiliation(s)
- Rafal Bartoszewski
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | | | | | | | | |
Collapse
|
25
|
Costello JL, Stead JA, Feigenbutz M, Jones RM, Mitchell P. The C-terminal region of the exosome-associated protein Rrp47 is specifically required for box C/D small nucleolar RNA 3'-maturation. J Biol Chem 2010; 286:4535-43. [PMID: 21135092 PMCID: PMC3039359 DOI: 10.1074/jbc.m110.162826] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Cells lacking the exosome-associated protein Rrp47 show similar defects in stable RNA processing to those observed in the absence of the catalytic subunit Rrp6, but the precise mechanism(s) by which Rrp47 functions together with Rrp6 remains unclear. Deletion complementation analyses defined an N-terminal region of Rrp47, largely coincident with the bioinformatically defined Sas10/C1D domain, which was sufficient for protein function in vivo. In vitro protein interaction studies demonstrated that this domain of Rrp47 binds the PMC2NT domain of Rrp6. Expression of the N-terminal domain of Rrp47 in yeast complemented most RNA-processing defects associated with the rrp47Δ mutant but failed to complement the defect observed in 3′-end maturation of box C/D small nucleolar RNAs. Consistent with these results, protein capture assays revealed an interaction between the C-terminal region of Rrp47 and the small nucleolar ribonucleoproteins Nop56 and Nop58. Filter binding assays demonstrated that deletion of the lysine-rich sequence at the C terminus of Rrp47 blocked RNA binding in vitro. Furthermore, a protein mutated both at the C terminus and within the N-terminal domain showed a synergistic defect in RNA binding without impacting on its ability to interact with Rrp6. These studies provide evidence for a role of Rrp47 in registering a small nucleolar ribonucleoprotein particle assembly, functionally characterize the Sas10/C1D domain of Rrp47, and show that both the C terminus of Rrp47 and the N-terminal domain contribute to its RNA-binding activity.
Collapse
Affiliation(s)
- Joe L Costello
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | | | | | | | | |
Collapse
|
26
|
Abstract
The Sas10/C1D domain is found in a small group of eukaryotic proteins that have functions in RNA processing events, translational control and DNA repair mechanisms. The domain is predicted to be alpha-helical in nature and comprises approx. 80 amino acid residues. Whereas the Sas10/C1D domain has yet to be functionally characterized, available results suggest that this domain forms a binding surface for specific interactions with other proteins and can concomitantly interact with RNA or DNA. This property of the Sas10/C1D domain may facilitate this family of proteins to dock other proteins on to nucleic acid substrates.
Collapse
|
27
|
When proteomics meets structural biology. Trends Biochem Sci 2010; 35:522-9. [DOI: 10.1016/j.tibs.2010.04.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 04/20/2010] [Accepted: 04/22/2010] [Indexed: 11/18/2022]
|
28
|
de Almeida SF, García-Sacristán A, Custódio N, Carmo-Fonseca M. A link between nuclear RNA surveillance, the human exosome and RNA polymerase II transcriptional termination. Nucleic Acids Res 2010; 38:8015-26. [PMID: 20699273 PMCID: PMC3001075 DOI: 10.1093/nar/gkq703] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In eukaryotes, the production of mature messenger RNA that exits the nucleus to be translated into protein in the cytoplasm requires precise and extensive modification of the nascent transcript. Any failure that compromises the integrity of an mRNA may cause its retention in the nucleus and trigger its degradation. Multiple studies indicate that mRNAs with processing defects accumulate in nuclear foci or ‘dots’ located near the site of transcription, but how exactly are defective RNAs recognized and tethered is still unknown. Here, we present evidence suggesting that unprocessed β-globin transcripts render RNA polymerase II (Pol II) incompetent for termination and that this quality control process requires the integrity of the nuclear exosome. Our results show that unprocessed pre-mRNAs remain tethered to the DNA template in association with Pol II, in an Rrp6-dependent manner. This reveals an unprecedented link between nuclear RNA surveillance, the exosome and Pol II transcriptional termination.
Collapse
Affiliation(s)
- Sérgio F de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | | | | | | |
Collapse
|
29
|
Karpinets TV, Romine MF, Schmoyer DD, Kora GH, Syed MH, Leuze MR, Serres MH, Park BH, Samatova NF, Uberbacher EC. Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2010; 2010:baq012. [PMID: 20627862 PMCID: PMC2911847 DOI: 10.1093/database/baq012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Shewanellae are facultative γ-proteobacteria whose remarkable respiratory versatility has resulted in interest in their utility for bioremediation of heavy metals and radionuclides and for energy generation in microbial fuel cells. Extensive experimental efforts over the last several years and the availability of 21 sequenced Shewanella genomes made it possible to collect and integrate a wealth of information on the genus into one public resource providing new avenues for making biological discoveries and for developing a system level understanding of the cellular processes. The Shewanella knowledgebase was established in 2005 to provide a framework for integrated genome-based studies on Shewanella ecophysiology. The present version of the knowledgebase provides access to a diverse set of experimental and genomic data along with tools for curation of genome annotations and visualization and integration of genomic data with experimental data. As a demonstration of the utility of this resource, we examined a single microarray data set from Shewanella oneidensis MR-1 for new insights into regulatory processes. The integrated analysis of the data predicted a new type of bacterial transcriptional regulation involving co-transcription of the intergenic region with the downstream gene and suggested a biological role for co-transcription that likely prevents the binding of a regulator of the upstream gene to the regulator binding site located in the intergenic region. Database URL:http://shewanella-knowledgebase.org:8080/Shewanella/ or http://spruce.ornl.gov:8080/Shewanella/
Collapse
|
30
|
Gruaz L, Delucinge-Vivier C, Descombes P, Dayer JM, Burger D. Blockade of T cell contact-activation of human monocytes by high-density lipoproteins reveals a new pattern of cytokine and inflammatory genes. PLoS One 2010; 5:e9418. [PMID: 20195532 PMCID: PMC2828473 DOI: 10.1371/journal.pone.0009418] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 02/06/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Cellular contact with stimulated T cells is a potent inducer of cytokine production in human monocytes and is likely to play a substantial part in chronic/sterile inflammatory diseases. High-density lipoproteins (HDL) specifically inhibit the production of pro-inflammatory cytokines induced by T cell contact. METHODOLOGY/PRINCIPAL FINDINGS To further elucidate the pro-inflammatory functions of cellular contact with stimulated T cells and its inhibition by HDL, we carried out multiplex and microarray analyses. Multiplex analysis of monocyte supernatant revealed that 12 out of 27 cytokines were induced upon contact with stimulated T cells, which cytokines included IL-1Ra, G-CSF, GM-CSF, IFNgamma, CCL2, CCL5, TNF, IL-1beta, IL-6, IL-8, CCL3, and CCL4, but only the latter six were inhibited by HDL. Microarray analysis showed that 437 out of 54,675 probe sets were enhanced in monocytes activated by contact with stimulated T cells, 164 probe sets (i.e., 38%) being inhibited by HDL. These results were validated by qPCR. Interestingly, the cytokines induced by T cell contact in monocytes comprised IL-1beta, IL-6 but not IL-12, suggesting that this mechanism might favor Th17 polarization, which emphasizes the relevance of this mechanism to chronic inflammatory diseases and highlights the contrast with acute inflammatory conditions that usually involve lipopolysaccharides (LPS). In addition, the expression of miR-155 and production of prostaglandin E(2)-both involved in inflammatory response-were triggered by T cell contact and inhibited in the presence of HDL. CONCLUSIONS/SIGNIFICANCE These results leave no doubt as to the pro-inflammatory nature of T cell contact-activation of human monocytes and the anti-inflammatory functions of HDL.
Collapse
Affiliation(s)
- Lyssia Gruaz
- Division of Immunology and Allergy, Inflammation and Allergy Research Group, Hans Wilsdorf Laboratory, Department of Internal Medicine and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | | | | | | |
Collapse
|
31
|
Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. Non-coding RNAs: regulators of disease. J Pathol 2010; 220:126-39. [PMID: 19882673 DOI: 10.1002/path.2638] [Citation(s) in RCA: 755] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
For 50 years the term 'gene' has been synonymous with regions of the genome encoding mRNAs that are translated into protein. However, recent genome-wide studies have shown that the human genome is pervasively transcribed and produces many thousands of regulatory non-protein-coding RNAs (ncRNAs), including microRNAs, small interfering RNAs, PIWI-interacting RNAs and various classes of long ncRNAs. It is now clear that these RNAs fulfil critical roles as transcriptional and post-transcriptional regulators and as guides of chromatin-modifying complexes. Here we review the biology of ncRNAs, focusing on the fundamental mechanisms by which ncRNAs facilitate normal development and physiology and, when dysfunctional, underpin disease. We also discuss evidence that intergenic regions associated with complex diseases express ncRNAs, as well as the potential use of ncRNAs as diagnostic markers and therapeutic targets. Taken together, these observations emphasize the need to move beyond the confines of protein-coding genes and highlight the fact that continued investigation of ncRNA biogenesis and function will be necessary for a comprehensive understanding of human disease.
Collapse
Affiliation(s)
- Ryan J Taft
- Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia
| | | | | | | | | |
Collapse
|
32
|
Turnover of Mature miRNAs and siRNAs in Plants and Algae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 700:124-39. [PMID: 21755478 DOI: 10.1007/978-1-4419-7823-3_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
microRNAs (miRNAs) and small interfering RNAs (siRNAs) play important roles in gene regulation and defense responses against transposons and viruses in eukaryotes. These small RNAs generally trigger the silencing of cognate sequences through a variety of mechanisms, including RNA degradation, translational inhibition and transcriptional repression. In the past few years, the synthesis and the mode of action of miRNAs and siRNAs have attracted great attention. However, relatively little is known about mechanisms of quality control during small RNA biogenesis as well as those that regulate mature small RNA stability. Recent studies in Arabidopsis thaliana and Caenorhabditis elegans have implicated 3'-to-5' (SDNs) and 5'-to-3' (XRN-2) exoribonucleases in mature miRNA turnover and the modulation of small RNA levels and activity. In the green alga Chlamydomonas reinhardtii, a nucleotidyltransferase (MUT68) and an exosome subunit (RRP6) are involved in the 3' untemplated uridylation and the degradation of miRNAs and siRNAs. The latter enzymes appear to function as a quality control mechanism to eliminate putative dysfunctional or damaged small RNA molecules. Several post-transcriptional modifications of miRNAs and siRNAs such as 3' terminal methylation and untemplated nucleotide additions have also been reported to affect small RNA stability. These collective findings are beginning to uncover a new layer of regulatory control in the pathways involving small RNAs. We anticipate that understanding the mechanisms of mature miRNA and siRNA turnover will have direct implications for fundamental biology as well as for applications of RNA interference technology.
Collapse
|
33
|
The Exosome and 3′–5′ RNA Degradation in Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 702:50-62. [DOI: 10.1007/978-1-4419-7841-7_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
34
|
Butler JS, Mitchell P. Rrp6, Rrp47 and Cofactors of the Nuclear Exosome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 702:91-104. [DOI: 10.1007/978-1-4419-7841-7_8] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|