1
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Button AC, Hall SD, Ashley EL, McHugh CA. Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA. RNA (NEW YORK, N.Y.) 2024; 30:240-255. [PMID: 38164599 PMCID: PMC10870365 DOI: 10.1261/rna.079713.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
XIST noncoding RNA promotes the initiation of X chromosome silencing by recruiting the protein SPEN to one X chromosome in female mammals. The SPEN protein is also called SHARP (SMRT and HDAC-associated repressor protein) and MINT (Msx-2 interacting nuclear target) in humans. SPEN recruits N-CoR2 and HDAC3 to initiate histone deacetylation on the X chromosome, leading to the formation of repressive chromatin marks and silencing gene expression. We dissected the contributions of different RNA and protein regions to the formation of a human XIST-SPEN complex in vitro and identified novel sequence and structure determinants that may contribute to X chromosome silencing initiation. Binding of SPEN to XIST RNA requires RRM 4 of the protein, in contrast to the requirement of RRM 3 and RRM 4 for specific binding to SRA RNA. Measurements of SPEN binding to full-length, dimeric, trimeric, or other truncated versions of the A-repeat region revealed that high-affinity binding of XIST to SPEN in vitro requires a minimum of four A-repeat segments. SPEN binding to XIST A-repeat RNA changes the accessibility of the RNA at specific nucleotide sequences, as indicated by changes in RNA reactivity through chemical structure probing. Based on computational modeling, we found that inter-repeat duplexes formed by multiple A-repeats can present an unpaired adenosine in the context of a double-stranded region of RNA. The presence of this specific combination of sequence and structural motifs correlates with high-affinity SPEN binding in vitro. These data provide new information on the molecular basis of the XIST and SPEN interaction.
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Affiliation(s)
- Aileen C Button
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Simone D Hall
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Ethan L Ashley
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Colleen A McHugh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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2
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Baleva MV, Piunova U, Chicherin I, Vasilev R, Levitskii S, Kamenski P. Mitochondrial Protein SLIRP Affects Biosynthesis of Cytochrome c Oxidase Subunits in HEK293T Cells. Int J Mol Sci 2023; 25:93. [PMID: 38203264 PMCID: PMC10779364 DOI: 10.3390/ijms25010093] [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: 11/18/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Mitochondria carry out various vital roles in eukaryotic cells, including ATP energy synthesis, the regulation of apoptosis, Fe-S cluster formation, and the metabolism of fatty acids, amino acids, and nucleotides. Throughout evolution, mitochondria lost most of their ancestor's genome but kept the replication, transcription, and translation machinery. Protein biosynthesis in mitochondria is specialized in the production of highly hydrophobic proteins encoded by mitochondria. These proteins are components of oxidative phosphorylation chain complexes. The coordination of protein synthesis must be precise to ensure the correct assembly of nuclear-encoded subunits for these complexes. However, the regulatory mechanisms of mitochondrial translation in human cells are not yet fully understood. In this study, we examined the contribution of the SLIRP protein in regulating protein biosynthesis in mitochondria. Using a click-chemistry approach, we discovered that deletion of the SLIRP gene disturbs mitochondrial translation, leading to the dysfunction of complexes I and IV, but it has no significant effect on complexes III and V. We have shown that this protein interacts only with the small subunit of the mitochondrial ribosome, which may indicate its involvement in the regulation of the mitochondrial translation initiation stage.
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Affiliation(s)
| | | | | | | | - Sergey Levitskii
- Faculty of Biology, Lomonosov Moscow State University, 1/12 Leninskie Gory, 119234 Moscow, Russia; (M.V.B.); (U.P.); (I.C.); (R.V.)
| | - Piotr Kamenski
- Faculty of Biology, Lomonosov Moscow State University, 1/12 Leninskie Gory, 119234 Moscow, Russia; (M.V.B.); (U.P.); (I.C.); (R.V.)
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3
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Fernando CD, Jayasekara WSN, Inampudi C, Kohonen-Corish MRJ, Cooper WA, Beilharz TH, Josephs TM, Garama DJ, Gough DJ. A STAT3 protein complex required for mitochondrial mRNA stability and cancer. Cell Rep 2023; 42:113033. [PMID: 37703176 DOI: 10.1016/j.celrep.2023.113033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/16/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) is a potent transcription factor necessary for life whose activity is corrupted in diverse diseases, including cancer. STAT3 biology was presumed to be entirely dependent on its activity as a transcription factor until the discovery of a mitochondrial pool of STAT3, which is necessary for normal tissue function and tumorigenesis. However, the mechanism of this mitochondrial activity remained elusive. This study uses immunoprecipitation and mass spectrometry to identify a complex containing STAT3, leucine-rich pentatricopeptide repeat containing (LRPPRC), and SRA stem-loop-interacting RNA-binding protein (SLIRP) that is required for the stability of mature mitochondrially encoded mRNAs and transport to the mitochondrial ribosome. Moreover, we show that this complex is enriched in patients with lung adenocarcinoma and that its deletion inhibits the growth of lung cancer in vivo, providing therapeutic opportunities through the specific targeting of the mitochondrial activity of STAT3.
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Affiliation(s)
- C Dilanka Fernando
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - W Samantha N Jayasekara
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Chaitanya Inampudi
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Maija R J Kohonen-Corish
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Woolcock Institute of Medical Research, Glebe, NSW 2037, Australia; School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; Faculty of Science, UTS Sydney, Ultimo, NSW 2007, Australia
| | - Wendy A Cooper
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia; Sydney Medical School, University of Sydney, Camperdown, NSW 2006, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Tracy M Josephs
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Daniel J Garama
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia.
| | - Daniel J Gough
- Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia.
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4
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Barmaki S, Al-Samadi A, Leskinen K, Wahbi W, Jokinen V, Vuoristo S, Salo T, Kere J, Wedenoja S, Saavalainen P. Transcriptomic Profiling of JEG-3 cells using human leiomyoma derived matrix. BIOMATERIALS AND BIOSYSTEMS 2022; 7:100056. [PMID: 36824489 PMCID: PMC9934486 DOI: 10.1016/j.bbiosy.2022.100056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/11/2022] [Accepted: 06/15/2022] [Indexed: 10/18/2022] Open
Abstract
Oxygen tension varies during placental and fetal development. Although hypoxia drives early trophoblast invasion, low placental oxygen levels during pregnancy show association with pregnancy complications including fetal growth restriction and preeclampsia. JEG-3 cells are often used as a trophoblast model. We studied transcriptional changes of JEG-3 cells on a uterine leiomyoma derived matrix Myogel. This might be the closest condition to the real uterine environment that we can get for an in vitro model. We observed that culturing JEG-3 cells on the leiomyoma matrix leads to strong stimulation of ribosomal pathways, energy metabolism, and ATP production. Furthermore, Myogel improved JEG-3 cell adherence in comparison to tissue culture treated plastic. We also included PDMS microchip hypoxia creation, and observed changes in oxidative phosphorylation, oxygen related genes and several hypoxia genes. Our study highlights the effects of Myogel matrix on growing JEG-3 cells, especially on mitochondria, energy metabolism, and protein synthesis.
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Affiliation(s)
- Samineh Barmaki
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland,Corresponding author.
| | - Ahmed Al-Samadi
- Department of Oral and Maxillofacial Disease, University of Helsinki, Helsinki 00290, Finland
| | - Katarzyna Leskinen
- Translational Immunology Research Program, and Department of Clinical and Medical Genetics, University of Helsinki, Helsinki 00290, Finland
| | - Wafa Wahbi
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Ville Jokinen
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, Espoo 00076, Finland
| | - Sanna Vuoristo
- Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland
| | - Tuula Salo
- Department of Oral and Maxillofacial Disease, University of Helsinki, Helsinki 00290, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14183, Sweden,Folkhälsan Research Center, Helsinki 00290, Finland,Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki 00014, Finland
| | - Satu Wedenoja
- Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki 00290, Finland,Stem Cells and Metabolism Research Program, University of Helsinki, and Folkhälsan Research Center, Helsinki 00290, Finland
| | - Päivi Saavalainen
- Translational Immunology Research Program, and Department of Clinical and Medical Genetics, University of Helsinki, Helsinki 00290, Finland,Folkhälsan Research Center, Helsinki 00290, Finland
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5
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Guo L, Engelen BPH, Hemel IMGM, de Coo IFM, Vreeburg M, Sallevelt SCEH, Hellebrekers DMEI, Jacobs EH, Sadeghi-Niaraki F, van Tienen FHJ, Smeets HJM, Gerards M. Pathogenic SLIRP variants as a novel cause of autosomal recessive mitochondrial encephalomyopathy with complex I and IV deficiency. Eur J Hum Genet 2021; 29:1789-1795. [PMID: 34426662 DOI: 10.1038/s41431-021-00947-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/09/2021] [Accepted: 08/10/2021] [Indexed: 12/26/2022] Open
Abstract
In a Dutch non-consanguineous patient having mitochondrial encephalomyopathy with complex I and complex IV deficiency, whole exome sequencing revealed two compound heterozygous variants in SLIRP. SLIRP gene encodes a stem-loop RNA-binding protein that regulates mitochondrial RNA expression and oxidative phosphorylation (OXPHOS). A frameshift and a deep-intronic splicing variant reduced the amount of functional wild-type SLIRP RNA to 5%. Consequently, in patient fibroblasts, MT-ND1, MT-ND6, and MT-CO1 expression was reduced. Lentiviral transduction of wild-type SLIRP cDNA in patient fibroblasts increased MT-ND1, MT-ND6, and MT-CO1 expression (2.5-7.2-fold), whereas mutant cDNAs did not. A fourfold decrease of citrate synthase versus total protein ratio in patient fibroblasts indicated that the resulting reduced mitochondrial mass caused the OXPHOS deficiency. Transduction with wild-type SLIRP cDNA led to a 2.4-fold increase of this ratio and partly restored OXPHOS activity. This confirmed causality of the SLIRP variants. In conclusion, we report SLIRP variants as a novel cause of mitochondrial encephalomyopathy with OXPHOS deficiency.
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Affiliation(s)
- Le Guo
- School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands.,Department of Toxicogenomics, Clinical Genomics Unit, Maastricht University, Maastricht, the Netherlands
| | - Bob P H Engelen
- Maastricht Center for Systems Biology (MacsBio), Maastricht University, Maastricht, the Netherlands
| | - Irene M G M Hemel
- Maastricht Center for Systems Biology (MacsBio), Maastricht University, Maastricht, the Netherlands
| | - Irenaeus F M de Coo
- School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands.,Department of Toxicogenomics, Clinical Genomics Unit, Maastricht University, Maastricht, the Netherlands
| | - Maaike Vreeburg
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Suzanne C E H Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Debby M E I Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Ed H Jacobs
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Farah Sadeghi-Niaraki
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Florence H J van Tienen
- School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands.,Department of Toxicogenomics, Clinical Genomics Unit, Maastricht University, Maastricht, the Netherlands
| | - Hubert J M Smeets
- School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands. .,Department of Toxicogenomics, Clinical Genomics Unit, Maastricht University, Maastricht, the Netherlands. .,School for Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, the Netherlands.
| | - Mike Gerards
- Maastricht Center for Systems Biology (MacsBio), Maastricht University, Maastricht, the Netherlands
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6
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Liang H, Liu J, Su S, Zhao Q. Mitochondrial noncoding RNAs: new wine in an old bottle. RNA Biol 2021; 18:2168-2182. [PMID: 34110970 DOI: 10.1080/15476286.2021.1935572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial noncoding RNAs (mt-ncRNAs) include noncoding RNAs inside the mitochondria that are transcribed from the mitochondrial genome or nuclear genome, and noncoding RNAs transcribed from the mitochondrial genome that are transported to the cytosol or nucleus. Recent findings have revealed that mt-ncRNAs play important roles in not only mitochondrial functions, but also other cellular activities. This review proposes a classification of mt-ncRNAs and outlines the emerging understanding of mitochondrial circular RNAs (mt-circRNAs), mitochondrial microRNAs (mitomiRs), and mitochondrial long noncoding RNAs (mt-lncRNAs), with an emphasis on their identification and functions.
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Affiliation(s)
- Huixin Liang
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jiayu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Shicheng Su
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Qiyi Zhao
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
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7
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Colella M, Cuomo D, Peluso T, Falanga I, Mallardo M, De Felice M, Ambrosino C. Ovarian Aging: Role of Pituitary-Ovarian Axis Hormones and ncRNAs in Regulating Ovarian Mitochondrial Activity. Front Endocrinol (Lausanne) 2021; 12:791071. [PMID: 34975760 PMCID: PMC8716494 DOI: 10.3389/fendo.2021.791071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/29/2021] [Indexed: 12/17/2022] Open
Abstract
The number of mitochondria in the oocyte along with their functions (e.g., energy production, scavenger activity) decline with age progression. Such multifaceted functions support several processes during oocyte maturation, ranging from energy supply to synthesis of the steroid hormones. Hence, it is hardly surprising that their impairment has been reported in both physiological and premature ovarian aging, wherein they are crucial players in the apoptotic processes that arise in aged ovaries. In any form, ovarian aging implies the progressive damage of the mitochondrial structure and activities as regards to ovarian germ and somatic cells. The imbalance in the circulating hormones and peptides (e.g., gonadotropins, estrogens, AMH, activins, and inhibins), active along the pituitary-ovarian axis, represents the biochemical sign of ovarian aging. Despite the progress accomplished in determining the key role of the mitochondria in preserving ovarian follicular number and health, their modulation by the hormonal signalling pathways involved in ovarian aging has been poorly and randomly explored. Yet characterizing this mechanism is pivotal to molecularly define the implication of mitochondrial dysfunction in physiological and premature ovarian aging, respectively. However, it is fairly difficult considering that the pathways associated with ovarian aging might affect mitochondria directly or by altering the activity, stability and localization of proteins controlling mitochondrial dynamics and functions, either unbalancing other cellular mediators, released by the mitochondria, such as non-coding RNAs (ncRNAs). We will focus on the mitochondrial ncRNAs (i.e., mitomiRs and mtlncRNAs), that retranslocate from the mitochondria to the nucleus, as active players in aging and describe their role in the nuclear-mitochondrial crosstalk and its modulation by the pituitary-ovarian hormone dependent pathways. In this review, we will illustrate mitochondria as targets of the signaling pathways dependent on hormones and peptides active along the pituitary/ovarian axis and as transducers, with a particular focus on the molecules retrieved in the mitochondria, mainly ncRNAs. Given their regulatory function in cellular activities we propose them as potential diagnostic markers and/or therapeutic targets.
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Affiliation(s)
- Marco Colella
- Biogem, Istituto di Biologia e Genetica Molecolare, Ariano Irpino, Italy
- Department of Science and Technology, University of Sannio, Benevento, Italy
- Laboratory of Pre-Clinical and Translational Research, IRCCS, Referral Cancer Center of Basilicata, Rionero in Vulture, Italy
| | - Danila Cuomo
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX, United States
| | - Teresa Peluso
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Ilaria Falanga
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Massimo Mallardo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, Naples, Italy
| | - Mario De Felice
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, Naples, Italy
- Istituto per l’ endocrinologia e l’oncologia “Gaetano Salvatore” (IEOS)-Centro Nazionale delle Ricerche (CNR), Naples, Italy
| | - Concetta Ambrosino
- Biogem, Istituto di Biologia e Genetica Molecolare, Ariano Irpino, Italy
- Department of Science and Technology, University of Sannio, Benevento, Italy
- Istituto per l’ endocrinologia e l’oncologia “Gaetano Salvatore” (IEOS)-Centro Nazionale delle Ricerche (CNR), Naples, Italy
- *Correspondence: Concetta Ambrosino,
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8
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Effects of SLIRP on Sperm Motility and Oxidative Stress. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9060356. [PMID: 33150185 PMCID: PMC7603556 DOI: 10.1155/2020/9060356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/15/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022]
Abstract
Background Deficient spermatozoon motility is one of the main causes of male infertility. However, there are still no accurate and effective treatments in a clinical setting for male asthenospermia. Exploring the genes and mechanism of asthenospermia has become one of the hot topics in reproductive medicine. Our aim is to study the effect of SLRIP on human spermatozoon motility and oxidative stress. Methods Sperm samples were collected including a normospermia group (60 cases) and an asthenospermia group (50 cases). SLIRP protein expression in spermatozoa was examined by western blotting, and relative mRNA expression of SLIRP in spermatozoa was quantified by reverse transcription polymerase chain reaction. Levels of reactive oxygen species (ROS), adenosine triphosphate (ATP) content, and the activity of manganese superoxide dismutase (MnSOD) in spermatozoa were also measured. Results The mRNA level and protein expression of SLIRP in the asthenospermia group were significantly reduced compared with those in the normospermia group. The ROS active oxygen level in the asthenospermia group significantly increased; however, the ATP content decreased significantly as well as the activity of MnSOD. Conclusion SLIRP regulates human male fertility, and SLIRP and sperm progressive motility are positively correlated. The expression of SLIRP is declined, oxidative damage is increased, and energy metabolism is decreased in spermatozoa of asthenospermia patients compared to normospermia participants.
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9
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Zhang Q, Cai S, Guo L, Zhao G. Propofol induces mitochondrial-associated protein LRPPRC and protects mitochondria against hypoxia in cardiac cells. PLoS One 2020; 15:e0238857. [PMID: 32898195 PMCID: PMC7478836 DOI: 10.1371/journal.pone.0238857] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
Background Hypoxia-induced oxidative stress is one of the main mechanisms of myocardial injury, which frequently results in cardiomyocyte death and precipitates life-threatening heart failure. Propofol (2,6-diisopropylphenol), which is used to sedate patients during surgery, was shown to strongly affect the regulation of physiological processes, including hypoxia-induced oxidative stress. However, the exact mechanism is still unclear. Methods Expression of LRPPRC, SLIRP, and Bcl-2 after propofol treatment was measured by RT-qPCR and western blot analyses. The effects of propofol under hypoxia were determine by assessing mitochondrial homeostasis and mitochondrial function, including the ATP level and mitochondrial mass. Autophagy/mitophagy was measured by detecting the presence of LC3B, and autophagosomes were observed by transmission microscopy Results Propofol treatment inhibited cleaved caspase-9 and caspase-3, indicating its inhibitory roles in mitochondrial-related apoptosis. Propofol treatment also transcriptionally activated LRPPRC, a mitochondrial-associated protein that exerts multiple functions by maintaining mitochondrial homeostasis, in a manner dependent on the presence of hypoxia-induced factor (HIF)-1α transcriptional activity in H9C2 and primary rat cardiomyocytes. LRPPRC induced by propofol maintained the mitochondrial membrane potential (MMP) and promoted mitochondrial function, including ATP synthesis and transcriptional activity. Furthermore, LRPPRC induced by propofol contributes, at least partially, to the inhibition of apoptotic cell death induced by hypoxia. Conclusion Taken together, our results indicate that LRPPRC may have a protective antioxidant effect by maintaining mitochondrial homoeostasis induced by propofol and provide new insight into the protective mechanism of propofol against oxidative stress.
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Affiliation(s)
- Qianlu Zhang
- Department of Anesthesiology, The First Affiliated Hospital of the University of South China, Hengyang, Hunan Province, P.R. China
| | - Shiwei Cai
- Cardiovascular Surgery, The First Affiliated Hospital of the University of South China, Hengyang, Hunan Province, P.R. China
| | - Liping Guo
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan City People’s Hospital, Qingyuan, Guangdong Province, P.R. China
| | - Guojun Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan City People’s Hospital, Qingyuan, Guangdong Province, P.R. China
- * E-mail:
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10
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Dossin F, Pinheiro I, Żylicz JJ, Roensch J, Collombet S, Le Saux A, Chelmicki T, Attia M, Kapoor V, Zhan Y, Dingli F, Loew D, Mercher T, Dekker J, Heard E. SPEN integrates transcriptional and epigenetic control of X-inactivation. Nature 2020; 578:455-460. [PMID: 32025035 PMCID: PMC7035112 DOI: 10.1038/s41586-020-1974-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/10/2020] [Indexed: 11/16/2022]
Abstract
Xist represents a paradigm for long non-coding RNA function in epigenetic regulation, although how it mediates X-chromosome inactivation (XCI) remains largely unexplained. Multiple Xist-RNA binding proteins have recently been identified, including SPEN1–3, the loss of which has been associated with deficient XCI at multiple loci2–6. Here we demonstrate that SPEN is a key orchestrator of XCI in vivo and unravel its mechanism of action. We show that SPEN is essential for initiating gene silencing on the X chromosome in preimplantation mouse embryos and embryonic stem cells. SPEN is dispensable for maintenance of XCI in neural progenitors, although it significantly dampens expression of genes that escape XCI. We show that SPEN is immediately recruited to the X-chromosome upon Xist up-regulation, and is targeted to enhancers and promoters of active genes. SPEN rapidly disengages from chromatin upon gene silencing, implying a need for active transcription to tether it to chromatin. We define SPEN’s SPOC domain as a major effector of SPEN’s gene silencing function, and show that tethering SPOC to Xist RNA is sufficient to mediate gene silencing. We identify SPOC’s protein partners which include NCOR/SMRT, the m6A RNA methylation machinery, the NuRD complex, RNA polymerase II and factors involved in regulation of transcription initiation and elongation. We propose that SPEN acts as a molecular integrator for initiation of XCI, bridging Xist RNA with the transcription machinery as well as nucleosome remodelers and histone deacetylases, at active enhancers and promoters.
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Affiliation(s)
- François Dossin
- European Molecular Biology Laboratory, Director's Unit, Heidelberg, Germany
| | - Inês Pinheiro
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France
| | - Jan J Żylicz
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Julia Roensch
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France
| | - Samuel Collombet
- European Molecular Biology Laboratory, Director's Unit, Heidelberg, Germany
| | - Agnès Le Saux
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France
| | - Tomasz Chelmicki
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France
| | - Mikaël Attia
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France
| | - Varun Kapoor
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Thomas Mercher
- INSERM U1170, Gustave Roussy Institute, Université Paris-Sud, Villejuif, France
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Edith Heard
- European Molecular Biology Laboratory, Director's Unit, Heidelberg, Germany. .,Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, Paris, France.
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11
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Interaction between androgen receptor and coregulator SLIRP is regulated by Ack1 tyrosine kinase and androgen. Sci Rep 2019; 9:18637. [PMID: 31819114 PMCID: PMC6901447 DOI: 10.1038/s41598-019-55057-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/23/2019] [Indexed: 12/16/2022] Open
Abstract
Aberrant activation of the androgen receptor (AR) may play a critical role in castration resistant prostate cancer. After ligand binding, AR is recruited to the androgen responsive element (ARE) sequences on the DNA where AR interaction with coactivators and corepressors modulates transcription. We demonstrated that phosphorylation of AR at Tyr-267 by Ack1/TNK2 tyrosine kinase results in nuclear translocation, DNA binding, and androgen-dependent gene transcription in a low androgen environment. In order to dissect downstream mechanisms, we searched for proteins whose interaction with AR was regulated by Ack1. SLIRP (SRA stem-loop interacting RNA binding protein) was identified as a candidate protein. Interaction between AR and SLIRP was disrupted by Ack1 kinase activity as well as androgen or heregulin treatment. The noncoding RNA, SRA, was required for AR-SLIRP interaction. SLIRP was bound to ARE’s of AR target genes in the absence of androgen. Treatment with androgen or heregulin led to dissociation of SLIRP from the ARE. Whole transcriptome analysis of SLIRP knockdown in androgen responsive LNCaP cells showed that SLIRP affects a significant subset of androgen-regulated genes. Our data suggest that Ack1 kinase and androgen regulate interaction between AR and SLIRP and that SLIRP functions as a coregulator of AR with properties of a corepressor in a context-dependent manner.
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12
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Li L, Miao W, Williams P, Guo C, Wang Y. SLIRP Interacts with Helicases to Facilitate 2'- O-Methylation of rRNA and to Promote Translation. J Am Chem Soc 2019; 141:10958-10961. [PMID: 31260285 DOI: 10.1021/jacs.9b04424] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SRA stem-loop-interacting RNA-binding protein (SLIRP) is a versatile protein that can interact with the stem-loop structure in RNA and with G quadruplex DNA. By using a quantitative proteomic experiment, we found that SLIRP interacts with the majority of the human helicase proteome. We also found that these interactions facilitate 2'-O-methylation of a number of nucleosides in rRNA and promote protein translation. Hence, we uncovered a novel function of SLIRP protein and offered novel mechanistic insights into its function as a RNA chaperone and into the regulation of 2'-O-methylation of rRNA.
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Affiliation(s)
- Lin Li
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
| | - Weili Miao
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
| | - Preston Williams
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
| | - Cheng Guo
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
| | - Yinsheng Wang
- Department of Chemistry , University of California Riverside , Riverside , California 92521-0403 , United States
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13
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Pardini B, Calin GA. MicroRNAs and Long Non-Coding RNAs and Their Hormone-Like Activities in Cancer. Cancers (Basel) 2019; 11:cancers11030378. [PMID: 30884898 PMCID: PMC6468345 DOI: 10.3390/cancers11030378] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/02/2019] [Accepted: 03/11/2019] [Indexed: 12/12/2022] Open
Abstract
Hormones are messengers circulating in the body that interact with specific receptors on the cell membrane or inside the cells and regulate, at a distal site, the activities of specific target organs. The definition of hormone has evolved in the last years. Hormones are considered in the context of cell–cell communication and mechanisms of cellular signaling. The best-known mechanisms of this kind are chemical receptor-mediated events, the cell–cell direct interactions through synapses, and, more recently, the extracellular vesicle (EV) transfer between cells. Recently, it has been extensively demonstrated that EVs are used as a way of communication between cells and that they are transporters of specific messenger signals including non-coding RNAs (ncRNAs) such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Circulating ncRNAs in body fluids and extracellular fluid compartments may have endocrine hormone-like effects because they can act at a distance from secreting cells with widespread consequences within the recipient cells. Here, we discuss and report examples of the potential role of miRNAs and lncRNAs as mediator for intercellular communication with a hormone-like mechanism in cancer.
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Affiliation(s)
- Barbara Pardini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, 1515 Holcombe Boulevard, Unit 422, Houston, TX 77030, USA.
- Department of Medical Sciences, University of Turin, Turin 10126, Italy.
- Italian Institute for Genomic Medicine (IIGM), Turin 10126, Italy.
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, 1515 Holcombe Boulevard, Unit 422, Houston, TX 77030, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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14
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Zheng Y, Wang Z, Zhu Y, Wang W, Bai M, Jiao Q, Wang Y, Zhao S, Yin X, Guo D, Bai W. LncRNA-000133 from secondary hair follicle of Cashmere goat: identification, regulatory network and its effects on inductive property of dermal papilla cells. Anim Biotechnol 2019; 31:122-134. [PMID: 30632899 DOI: 10.1080/10495398.2018.1553788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs), a class of non-protein conding RNAs > 200 nt in length, were thought to play critical roles in regulating the expression of protein-coding genes. Here, we identified and characterized a novel lncRNA-000133 from the secondary hair follicle (SHF) of cashmere goat with its ceRNA network analysis, as well as, its potential effects on inductive property of dermal papilla cells were evaluated through overexpression analysis. Expression analysis indicated that lncRNA-000133 had a significantly higher expression at anagen than that at telogen in SHF of Cashmere goat, suggesting that lncRNA-000133 might be involved in the reconstruction of SHF with the formation and growth of cashmere fiber. Taken together with methylation analysis, we showed that 5' regulatory region methylation of the lncRNA-000133 gene might be involved in its expression suppression in SHF of Cashmere goat. The ceRNA regulatory network showed that a rich and complex regulatory relationship between lncRNA-000133 and related miRNAs with their target genes. The overexpression of lncRNA-000133 led to a significant increasing in the relative expression of ET-1, SCF, ALP and LEF1 in dermal papilla cells suggesting that lncRNA-000133 appears to contribute the inductive property of dermal papilla cells.
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Affiliation(s)
- Yuanyuan Zheng
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yubo Zhu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Wei Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Man Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Qian Jiao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yanru Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Sujun Zhao
- Sichuan Animal Science Academy, Chengdu, P. R. China
| | - Xianbo Yin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Dan Guo
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang, P. R. China
| | - Wenlin Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
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15
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Ji E, Kim C, Kim W, Lee EK. Role of long non-coding RNAs in metabolic control. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1863:194348. [PMID: 30594638 DOI: 10.1016/j.bbagrm.2018.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/21/2018] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as pivotal regulators of gene expression by influencing various biological processes including proliferation, apoptosis, differentiation, and senescence. Accumulating evidence implicates lncRNAs in the maintenance of metabolic homeostasis; dysregulation of certain lncRNAs promotes the progression of metabolic disorders such as diabetes, obesity, and cardiovascular diseases. In this review, we discuss our understanding of lncRNAs implicated in metabolic control, focusing on in particular diseases arising from chronic inflammation, insulin resistance, and lipid homeostasis. We have analyzed lncRNAs and their molecular targets involved in the pathogenesis of chronic liver disease, diabetes, and obesity, and have discussed the rising interest in lncRNAs as diagnostic and therapeutic targets improving metabolic homeostasis. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.
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Affiliation(s)
- Eunbyul Ji
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, South Korea
| | - Chongtae Kim
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, South Korea
| | - Wook Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, South Korea
| | - Eun Kyung Lee
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, South Korea.
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16
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Estrogen receptor β upregulated by lncRNA-H19 to promote cancer stem-like properties in papillary thyroid carcinoma. Cell Death Dis 2018; 9:1120. [PMID: 30389909 PMCID: PMC6214949 DOI: 10.1038/s41419-018-1077-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 08/19/2018] [Accepted: 09/13/2018] [Indexed: 12/18/2022]
Abstract
Estrogen receptor β (ERβ) plays critical roles in thyroid cancer progression. However, its role in thyroid cancer stem cell maintenance remains elusive. Here, we report that ERβ is overexpressed in papillary thyroid cancer stem cells (PTCSCs), whereas ablation of ERβ decreases stemness-related factors expression, diminishes ALDH+ cell populations, and suppresses sphere formation ability and tumor growth. Screening estrogen-responsive lncRNAs in PTC spheroid cells, we find that lncRNA-H19 is highly expressed in PTCSCs and PTC tissue specimens, which is correlated with poor overall survival. Mechanistically, estradiol (E2) significantly promotes H19 transcription via ERβ and elevates H19 expression. Silencing of H19 inhibits E2-induced sphere formation ability. Furthermore, H19 acting as a competitive endogenous RNA sequesters miRNA-3126-5p to reciprocally release ERβ expression. ERβ depletion reverses H19-induced stem-like properties upon E2 treatment. Appropriately, ERβ is upregulated in PTC tissue specimens. Notably, aspirin attenuates E2-induced cancer stem-like traits through decreasing both H19 and ERβ expression. Collectively, our findings reveal that ERβ-H19 positive feedback loop has a compelling role in PTCSC maintenance under E2 treatment and provides a potential therapeutic targeting strategy for PTC.
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17
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Sheng L, Ye L, Zhang D, Cawthorn WP, Xu B. New Insights Into the Long Non-coding RNA SRA: Physiological Functions and Mechanisms of Action. Front Med (Lausanne) 2018; 5:244. [PMID: 30238005 PMCID: PMC6135885 DOI: 10.3389/fmed.2018.00244] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNA) are emerging as new genetic/epigenetic regulators that can impact almost all physiological functions. Here, we focus on the long non-coding steroid receptor RNA activator (SRA), including new insights into its effects on gene expression, the cell cycle, and differentiation; how these relate to physiology and disease; and the mechanisms underlying these effects. We discuss how SRA acts as an RNA coactivator in nuclear receptor signaling; its effects on steroidogenesis, adipogenesis, and myocyte differentiation; the impact on breast and prostate cancer tumorigenesis; and, finally, its ability to modulate hepatic steatosis through several signaling pathways. Genome-wide analysis reveals that SRA regulates hundreds of target genes in adipocytes and breast cancer cells and binds to thousands of genomic sites in human pluripotent stem cells. Recent studies indicate that SRA acts as a molecular scaffold and forms networks with numerous coregulators and chromatin-modifying regulators in both activating and repressive complexes. We discuss how modifications to SRA's unique stem-loop secondary structure are important for SRA function, and highlight the various SRA isoforms and mutations that have clinical implications. Finally, we discuss the future directions for better understanding the molecular mechanisms of SRA action and how this might lead to new diagnostic and therapeutic approaches.
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Affiliation(s)
- Liang Sheng
- Department of Pharmacology, School of Basic Medical Science, Nanjing Medical University, Nanjing, China.,Neuroprotective Drug Discovery Key Laboratory of Nanjing Medical University, Nanjing, China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Dong Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - William P Cawthorn
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Bin Xu
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan Medical Center Ann Arbor, MI, United States
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18
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Korfanty J, Stokowy T, Chadalski M, Toma-Jonik A, Vydra N, Widłak P, Wojtaś B, Gielniewski B, Widlak W. SPEN protein expression and interactions with chromatin in mouse testicular cells. Reproduction 2018; 156:195-206. [DOI: 10.1530/rep-18-0046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/07/2018] [Indexed: 12/17/2022]
Abstract
SPEN (spen family transcription repressor) is a nucleic acid-binding protein putatively involved in repression of gene expression. We hypothesized that SPEN could be involved in general downregulation of the transcription during the heat shock response in mouse spermatogenic cells through its interactions with chromatin. We documented predominant nuclear localization of the SPEN protein in spermatocytes and round spermatids, which was retained after heat shock. Moreover, the protein was excluded from the highly condensed chromatin. Chromatin immunoprecipitation experiments clearly indicated interactions of SPEN with chromatinin vivo. However, ChIP-Seq analyses did not reveal any strong specific peaks both in untreated and heat shocked cells, which might suggest dispersed localization of SPEN and/or its indirect binding to DNA. Usingin situproximity ligation assay we found closein vivoassociations of SPEN with MTA1 (metastasis-associated 1), a member of the nucleosome remodeling complex with histone deacetylase activity, which might contribute to interactions of SPEN with chromatin.
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19
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Klinge CM. Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers. Endocr Relat Cancer 2018; 25:R259-R282. [PMID: 29440232 DOI: 10.1530/erc-17-0548] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/12/2018] [Indexed: 12/11/2022]
Abstract
The human genome is 'pervasively transcribed' leading to a complex array of non-coding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation. Long non-coding RNAs (lncRNAs) are classified as >200 nucleotides in length, but range up to several kb and are heterogeneous in genomic origin and function. lncRNAs fold into structures that interact with DNA, RNA and proteins to regulate chromatin dynamics, protein complex assembly, transcription, telomere biology and splicing. Some lncRNAs act as sponges for miRNAs and decoys for proteins. Nuclear-encoded lncRNAs can be taken up by mitochondria and lncRNAs are transcribed from mtDNA. Both miRNAs and lncRNAs are dysregulated in endocrine cancers. This review provides an overview on the current understanding of the regulation and function of selected lncRNAs and miRNAs, and their interaction, in endocrine-related cancers: breast, prostate, endometrial and thyroid.
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20
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Williams P, Li L, Dong X, Wang Y. Identification of SLIRP as a G Quadruplex-Binding Protein. J Am Chem Soc 2017; 139:12426-12429. [PMID: 28859475 DOI: 10.1021/jacs.7b07563] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The guanine quadruplex (G4) structure in DNA is a secondary structure motif that plays important roles in DNA replication, transcriptional regulation, and maintenance of genomic stability. Here, we employed a quantitative mass spectrometry-based approach to profile the interaction proteomes of three well-defined G4 structures derived from the human telomere and the promoters of cMYC and cKIT genes. We identified SLIRP as a novel G4-interacting protein. We also demonstrated that the protein could bind directly with G4 DNA with Kd values in the low nanomolar range and revealed that the robust binding of the protein toward G4 DNA requires its RRM domain. We further assessed, by using CRISPR-Cas9-introduced affinity tag and ChIP-Seq analysis, the genome-wide occupancy of SLIRP, and showed that the protein binds preferentially to G-rich DNA sequences that can fold into G4 structures. Together, our results uncovered a novel cellular protein that can interact directly with G4 DNA, which underscored the complex regulatory networks involved in G4 biology.
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Affiliation(s)
- Preston Williams
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
| | - Xiaoli Dong
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
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21
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Dong Y, Yoshitomi T, Hu JF, Cui J. Long noncoding RNAs coordinate functions between mitochondria and the nucleus. Epigenetics Chromatin 2017; 10:41. [PMID: 28835257 PMCID: PMC5569521 DOI: 10.1186/s13072-017-0149-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 08/17/2017] [Indexed: 11/23/2022] Open
Abstract
In animal cells, mitochondria are the primary powerhouses and metabolic factories. They also contain genomes and can produce mitochondrial-specific nucleic acids and proteins. To maintain homeostasis of the entire cell, an intense cross-talk between mitochondria and the nucleus, mediated by encoded noncoding RNAs (ncRNAs), as well as proteins, is required. Long ncRNAs (lncRNAs) contain characteristic structures, and they are involved in the regulation of almost every stage of gene expression, as well as being implicated in a variety of disease states, such as cancer. In the coordinated signaling system, several lncRNAs, transcribed in the nucleus but residing in mitochondria, play a key role in regulating mitochondrial functions or dynamics. For example, RMRP, a component of the mitochondrial RNase MRP, is important for mitochondrial DNA replication and RNA processing, and the steroid receptor RNA activator, SRA, is a key modulator of hormone signaling and is present in both the nucleus and mitochondria. Some RNA-binding proteins maybe play a role in the lncRNAs transport system, such as HuR, GRSF1, SHARP, SLIRP, PPR, and PNPASE. Furthermore, a series of nuclear DNA-encoded lncRNAs were implicated in mitochondria-mediated apoptosis, mitochondrial bioenergetics and biosynthesis, and glutamine metabolism. The mitochondrial genome can also encode a set of lncRNAs, and they are divided into three categories: (1) lncND5, lncND6, and lncCyt b RNA; (2) chimeric mitochondrial DNA-encoded lncRNAs; and (3) putative mitochondrial DNA-encoded lncRNAs. It has been reported that the mitochondrial DNA-encoded lncRNAs appear to operate in the nucleus. The molecular mechanisms underlying trafficking of the mitochondrial DNA-encoded lncRNAs to the nucleus in mammals are only now beginning to emerge. In conclusion, both nuclear- and mitochondrial DNA-encoded lncRNAs mediate an intense intercompartmental cross-talk, which opens a rich field for investigation of the mechanism underlying the intercompartmental coordination and the maintenance of whole cell homeostasis.
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Affiliation(s)
- Yaru Dong
- Department of Ophthalmology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA, 94304, USA
| | - Takeshi Yoshitomi
- Department of Ophthalmology, Akita University School of Medicine, 1-1-1 Hondo, Akita, 010-8543, Japan
| | - Ji-Fan Hu
- Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA, 94304, USA. .,Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, Changchun, 130061, Jilin, China.
| | - Jizhe Cui
- Department of Ophthalmology, The Second Hospital of Jilin University, 218 Ziqiang Street, Changchun, 130041, Jilin, China.
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22
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Chen G, Yu D, Nian X, Liu J, Koenig RJ, Xu B, Sheng L. LncRNA SRA promotes hepatic steatosis through repressing the expression of adipose triglyceride lipase (ATGL). Sci Rep 2016; 6:35531. [PMID: 27759039 PMCID: PMC5069493 DOI: 10.1038/srep35531] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 09/30/2016] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD), the most common form of chronic liver disease, manifests as an over-accumulation of hepatic fat. We have recently shown that mice with genetic knockout of a long non-coding RNA (lncRNA) steroid receptor RNA activator (SRA) (SRAKO) are resistant to high fat diet-induced obesity with a phenotype that includes improved glucose tolerance and attenuated hepatic steatosis. The underlying mechanism was investigated in the present study. We found that hepatic levels of SRA and adipose triglyceride lipase (ATGL), a major hepatic triacylglycerol (TAG) hydrolase, were inversely regulated by fasting in mice, and the expression of liver ATGL was induced by SRAKO under normal and high fat diet (HFD) feeding. Loss of SRA in primary hepatocytes or a hepatocyte cell line upregulates, but forced expression of SRA inhibits ATGL expression and free fatty acids (FFA) β-oxidation. SRA inhibits ATGL promoter activity, primarily by inhibiting the otherwise-inductive effects of the transcription factor, forkhead box protein O1 (FoxO1). Our data reveal a novel function of SRA in promoting hepatic steatosis through repression of ATGL expression.
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Affiliation(s)
- Gang Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Dongsheng Yu
- Department of Pharmacology, School of Basic Medical Science, Nanjing Medical University, 140 Hanzhong Rd., Nanjing, Jiangsu, 210029, China
| | - Xue Nian
- Department of Pharmacology, School of Basic Medical Science, Nanjing Medical University, 140 Hanzhong Rd., Nanjing, Jiangsu, 210029, China
| | - Junyi Liu
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ronald J Koenig
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, MI 48109-5678, USA
| | - Bin Xu
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical Center, Ann Arbor, MI 48109-5678, USA
| | - Liang Sheng
- Department of Pharmacology, School of Basic Medical Science, Nanjing Medical University, 140 Hanzhong Rd., Nanjing, Jiangsu, 210029, China
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23
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Abstract
An individual's risk of developing a common disease typically depends on an interaction of genetic and environmental factors. Epigenetic research is uncovering novel ways through which environmental factors such as diet, air pollution, and chemical exposure can affect our genes. DNA methylation and histone modifications are the most commonly studied epigenetic mechanisms. The role of long non-coding RNAs (lncRNAs) in epigenetic processes has been more recently highlighted. LncRNAs are defined as transcribed RNA molecules greater than 200 nucleotides in length with little or no protein-coding capability. While few functional lncRNAs have been well characterized to date, they have been demonstrated to control gene regulation at every level, including transcriptional gene silencing via regulation of the chromatin structure and DNA methylation. This review aims to provide a general overview of lncRNA function with a focus on their role as key regulators of health and disease and as biomarkers of environmental exposure.
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Affiliation(s)
- Oskar Karlsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, 171 76, Stockholm, Sweden.
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
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24
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Steroid receptor RNA activator: Biologic function and role in disease. Clin Chim Acta 2016; 459:137-146. [DOI: 10.1016/j.cca.2016.06.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/05/2016] [Accepted: 06/05/2016] [Indexed: 12/25/2022]
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25
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Foulds CE, Panigrahi AK, Coarfa C, Lanz RB, O'Malley BW. Long Noncoding RNAs as Targets and Regulators of Nuclear Receptors. Curr Top Microbiol Immunol 2016; 394:143-76. [PMID: 26362934 DOI: 10.1007/82_2015_465] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Intensive research has been directed at the discovery, biogenesis, and expression patterns of long noncoding RNAs , yet their biochemical functions have remained elusive for the most part. Nuclear receptors that interpret signaling mediated by small molecule hormones play a role in regulating the expression of some long noncoding RNAs. More importantly, these RNAs have also been shown to effect hormone-affected gene transcription regulated by the nuclear receptors. In this chapter, we summarize the current knowledge that has been acquired on hormonal signaling inducing expression of long noncoding RNAs and how they then may act in trans or in cis to modulate gene transcription. We highlight a few of these noncoding RNA molecules in terms of how they may impact hormone-driven cancers. Future directions critical for moving this field forward are presented, with a clear emphasis on the need for better biochemical approaches to address the mechanism of action of these exciting RNAs.
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Affiliation(s)
- Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Anil K Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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26
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Jung E, Jang S, Lee J, Kim Y, Shin H, Park HS, Lee Y. Truncated SRA RNA derivatives inhibit estrogen receptor-α-mediated transcription. Mol Biol Rep 2016; 43:1019-25. [PMID: 27406387 DOI: 10.1007/s11033-016-4039-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/06/2016] [Indexed: 10/21/2022]
Abstract
The steroid receptor RNA activator (SRA) is a long non-coding RNA (lncRNA) that acts as a putative coactivator for steroid receptor-mediated transcription. A recent study showed that SRA RNA can be structurally dissected into four domains comprising various secondary structures, but the contribution of each domain to the coactivation ability of SRA RNA was previously unknown. Here, we assessed the functional contributions of the various domains of SRA. We examined the effects of each domain on the coactivation of estrogen receptor-α (ERα)-mediated transcription of a luciferase reporter gene in HeLa cells. Then the detailed domain analysis was focused on domain III (D3) not only with the reporter gene in HeLa cells, but also with ERα-responsive genes in MCF7 breast cancer cells. Domain deletion analysis showed that the deletion of any domain decreased the luciferase activity, and that deletion of D3 caused the largest decrease. This D3 deletion effect was not recovered by co-expression of D3 alone; moreover, the expression of D3 fragments (particularly helices H15-H18, which are highly conserved across vertebrates) inhibited luciferase expression in HeLa cells. Moreover, a fragment containing helices H15-H18 reduced ERα-responsive gene expression in MCF7 breast cancer cells. Our findings indicate that D3 inhibited ERα-mediated transcription of a reporter gene in HeLa cells and that helices H15-H18, as a core element responsible for the D3-driven inhibition, reduced expression of ERα-responsive genes in breast cancer cells.
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Affiliation(s)
- Euihan Jung
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Seonghui Jang
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Jungmin Lee
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Youngmi Kim
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Heegwon Shin
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Hee-Sung Park
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon, 305-701, Korea.
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27
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Obeid JP, Zafar N, El Hokayem J. Steroid Hormone Receptor Coregulators in Endocrine Cancers. IUBMB Life 2016; 68:504-15. [PMID: 27240871 DOI: 10.1002/iub.1517] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/11/2016] [Accepted: 05/11/2016] [Indexed: 01/14/2023]
Abstract
Coregulators span a broad and extensive domain in modulating cellular transcriptional activity. Studies have established a dynamic role for such coregulators in various endocrine cancers. Steroid hormone receptors (SHRs) play a pivotal role in such endocrine cancers, and interact abundantly with transcriptional coregulators in altering gene expression. Several families of coregulators have implications in propagating the development, progression and invasion of breast, prostate, and other hormone-responsive cancers. This mini-review aims to discuss different classes of coregulators involved in endocrine cancers and highlight unique information regarding each family with relevance to mechanism, intervention, and novel directions being investigated. © 2016 IUBMB Life, 68(7):504-515, 2016.
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Affiliation(s)
- Jean-Pierre Obeid
- Department of Biochemistry and Molecular Biology, University of Miami, FL, USA
| | - Nawal Zafar
- Department of Biochemistry and Molecular Biology, University of Miami, FL, USA
| | - Jimmy El Hokayem
- Department of Biochemistry and Molecular Biology, University of Miami, FL, USA
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28
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Kurokawa R. Long noncoding RNA as a regulator for transcription. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2016; 51:29-41. [PMID: 21287132 DOI: 10.1007/978-3-642-16502-3_2] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Investigation of noncoding RNAs is in rapid progress, especially regarding translational repression by small (short) noncoding RNAs like microRNAs with 20-25 nucleotide-lengths, while long noncoding RNAs with nucleotide length of more than two hundred are also emerging. Indeed, our analysis has revealed that a long noncoding RNA transcribed from cyclin D1 promoter of 200 and 300 nucleotides exerts transcriptional repression through its binding protein TLS instead of translational repression. Translational repression is executed by short noncoding RNAs, while transcriptional repression is mainly done by long noncoding RNAs. These long noncoding RNAs are heterogeneous molecules and employ divergent molecular mechanisms to exert transcriptional repression. In this review, I overview recent publications regarding the transcription regulation by long noncoding RNAs and explore their biological significance. In addition, the relation between a random transcriptional activity of RNA polymerase II and the origin of long noncoding RNAs is discussed.
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Affiliation(s)
- Riki Kurokawa
- Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Hidaka-shi, Saitama-Ken, 350-1241, Japan,
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29
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Affinity purification-mass spectrometry analysis of bcl-2 interactome identified SLIRP as a novel interacting protein. Cell Death Dis 2016; 7:e2090. [PMID: 26866271 PMCID: PMC4849145 DOI: 10.1038/cddis.2015.357] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 02/06/2023]
Abstract
Members of the bcl-2 protein family share regions of sequence similarity, the bcl-2 homology (BH) domains. Bcl-2, the most studied member of this family, has four BH domains, BH1–4, and has a critical role in resistance to antineoplastic drugs by regulating the mitochondrial apoptotic pathway. Moreover, it is also involved in other relevant cellular processes such as tumor progression, angiogenesis and autophagy. Deciphering the network of bcl-2-interacting factors should provide a critical advance in understanding the different functions of bcl-2. Here, we characterized bcl-2 interactome by mass spectrometry in human lung adenocarcinoma cells. In silico functional analysis associated most part of the identified proteins to mitochondrial functions. Among them we identified SRA stem–loop interacting RNA-binding protein, SLIRP, a mitochondrial protein with a relevant role in regulating mitochondrial messenger RNA (mRNA) homeostasis. We validated bcl-2/SLIRP interaction by immunoprecipitation and immunofluorescence experiments in cancer cell lines from different histotypes. We showed that, although SLIRP is not involved in mediating bcl-2 ability to protect from apoptosis and oxidative damage, bcl-2 binds and stabilizes SLIRP protein and regulates mitochondrial mRNA levels. Moreover, we demonstrated that the BH4 domain of bcl-2 has a role in maintaining this binding.
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30
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Taylor DH, Chu ETJ, Spektor R, Soloway PD. Long non-coding RNA regulation of reproduction and development. Mol Reprod Dev 2015; 82:932-56. [PMID: 26517592 PMCID: PMC4762656 DOI: 10.1002/mrd.22581] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) have long been known to play vital roles in eukaryotic gene regulation. Studies conducted over a decade ago revealed that maturation of spliced, polyadenylated coding mRNA occurs by reactions involving small nuclear RNAs and small nucleolar RNAs; mRNA translation depends on activities mediated by transfer RNAs and ribosomal RNAs, subject to negative regulation by micro RNAs; transcriptional competence of sex chromosomes and some imprinted genes is regulated in cis by ncRNAs that vary by species; and both small-interfering RNAs and piwi-interacting RNAs bound to Argonaute-family proteins regulate post-translational modifications on chromatin and local gene expression states. More recently, gene-regulating noncoding RNAs have been identified, such as long intergenic and long noncoding RNAs (collectively referred to as lncRNAs)--a class totaling more than 100,000 transcripts in humans, which include some of the previously mentioned RNAs that regulate dosage compensation and imprinted gene expression. Here, we provide an overview of lncRNA activities, and then review the role of lncRNAs in processes vital to reproduction, such as germ cell specification, sex determination and gonadogenesis, sex hormone responses, meiosis, gametogenesis, placentation, non-genetic inheritance, and pathologies affecting reproductive tissues. Results from many species are presented to illustrate the evolutionarily conserved processes lncRNAs are involved in.
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Affiliation(s)
- David H. Taylor
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
| | - Erin Tsi-Jia Chu
- Field of Comparative Biomedical Sciences, Cornell University, Ithaca, New York
| | - Roman Spektor
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
| | - Paul D. Soloway
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
- Field of Comparative Biomedical Sciences, Cornell University, Ithaca, New York
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
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31
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Macaulay AD, Gilbert I, Scantland S, Fournier E, Ashkar F, Bastien A, Saadi HAS, Gagné D, Sirard MA, Khandjian ÉW, Richard FJ, Hyttel P, Robert C. Cumulus Cell Transcripts Transit to the Bovine Oocyte in Preparation for Maturation. Biol Reprod 2015; 94:16. [PMID: 26586844 PMCID: PMC4809558 DOI: 10.1095/biolreprod.114.127571] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 11/13/2015] [Indexed: 11/30/2022] Open
Abstract
So far, the characteristics of a good quality egg have been elusive, similar to the nature of the physiological, cellular, and molecular cues leading to its production both in vivo and in vitro. Current understanding highlights a strong and complex interdependence between the follicular cells and the gamete. Secreted factors induce cellular responses in the follicular cells, and direct exchange of small molecules from the cumulus cells to the oocyte through gap junctions controls meiotic arrest. Studying the interconnection between the cumulus cells and the oocyte, we previously demonstrated that the somatic cells also contribute transcripts to the gamete. Here, we show that these transcripts can be visualized moving down the transzonal projections (TZPs) to the oocyte, and that a time course analysis revealed progressive RNA accumulation in the TZPs, indicating that RNA transfer occurs before the initiation of meiosis resumption under a timetable fitting with the acquisition of developmental competence. A comparison of the identity of the nascent transcripts trafficking in the TZPs, with those in the oocyte increasing in abundance during maturation, and that are present on the oocyte's polyribosomes, revealed transcripts common to all three fractions, suggesting the use of transferred transcripts for translation. Furthermore, the removal of potential RNA trafficking by stripping the cumulus cells caused a significant reduction in maturation rates, indicating the need for the cumulus cell RNA transfer to the oocyte. These results offer a new perspective to the determinants of oocyte quality and female fertility, as well as provide insight that may eventually be used to improve in vitro maturation conditions.
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Affiliation(s)
- Angus D Macaulay
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Sara Scantland
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Eric Fournier
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Fazl Ashkar
- Department of Biomedical Sciences, Reproductive Biology Lab, University of Guelph, Guelph, Ontario, Canada
| | - Alexandre Bastien
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Habib A Shojaei Saadi
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Dominic Gagné
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Marc-André Sirard
- Département de Psychiatrie et Neurosciences, Institut universitaire en santé mentale de Québec, Université Laval, Québec City, Québec, Canada
| | - Édouard W Khandjian
- Département de Psychiatrie et Neurosciences, Institut universitaire en santé mentale de Québec, Université Laval, Québec City, Québec, Canada
| | - François J Richard
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
| | - Poul Hyttel
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claude Robert
- Département des sciences animales, Centre de recherche en biologie de la reproduction, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Québec, Canada
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32
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Yan Y, Cooper C, Hamedani MK, Guppy B, Xu W, Tsuyuki D, Zhang C, Nugent Z, Blanchard A, Davie JR, McManus K, Murphy LC, Myal Y, Leygue E. The steroid receptor RNA activator protein (SRAP) controls cancer cell migration/motility. FEBS Lett 2015; 589:4010-8. [PMID: 26581859 DOI: 10.1016/j.febslet.2015.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 11/03/2015] [Accepted: 11/05/2015] [Indexed: 11/15/2022]
Abstract
The steroid receptor RNA activator gene (SRA1) produces both a functional RNA (SRA) and a protein (SRAP), whose exact physiological roles remain unknown. To identify cellular processes regulated by SRAP we compared the transcriptome of Hela and MDA-MB-231 cancer cells upon depletion of the SRA/SRAP transcripts or overexpression of the SRAP protein. RNA-seq and Ontology analyses pinpointed cellular movement as potentially regulated by SRAP. Using live cell imaging, we found that SRA/SRAP depletion and SRAP overexpression lead respectively to a decrease and increase in cancer cell motility. Our results highlight for the first time a link existing between SRA1 gene expression and cell motility.
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Affiliation(s)
- Yi Yan
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 770 Bannatyne Avenue, R3E0W3 Winnipeg, Manitoba, Canada
| | - Charlton Cooper
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada
| | - Mohammad K Hamedani
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 770 Bannatyne Avenue, R3E0W3 Winnipeg, Manitoba, Canada
| | - Brent Guppy
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 770 Bannatyne Avenue, R3E0W3 Winnipeg, Manitoba, Canada
| | - Wayne Xu
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada
| | - Deborah Tsuyuki
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada
| | - Christine Zhang
- Department of Immunology, University of Manitoba, 413 Apotex Center, 750 McDermot Ave., R3E0T5 Winnipeg, Manitoba, Canada
| | - Zoann Nugent
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada
| | - Anne Blanchard
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada; Department of Physiology, University of Manitoba, 770 Bannatyne Avenue, R3E0W3 Winnipeg, Manitoba, Canada
| | - James R Davie
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 770 Bannatyne Avenue, R3E0W3 Winnipeg, Manitoba, Canada
| | - Kirk McManus
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 770 Bannatyne Avenue, R3E0W3 Winnipeg, Manitoba, Canada
| | - Leigh C Murphy
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 770 Bannatyne Avenue, R3E0W3 Winnipeg, Manitoba, Canada
| | - Yvonne Myal
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada; Department of Physiology, University of Manitoba, 770 Bannatyne Avenue, R3E0W3 Winnipeg, Manitoba, Canada
| | - Etienne Leygue
- Manitoba Institute of Cell Biology, 675 McDermot Ave., R3E0V9 Winnipeg, Manitoba, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 770 Bannatyne Avenue, R3E0W3 Winnipeg, Manitoba, Canada.
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33
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Abstract
Long non-coding RNAs (lncRNAs) are a large and diverse group of RNAs that are often lineage-specific and that regulate multiple biological functions. Many are nuclear and are essential parts of ribonucleoprotein complexes that modify chromatin segments and establish active or repressive chromatin states; others are cytosolic and regulate the stability of mRNA or act as microRNA sponges. This Review summarizes the current knowledge of lncRNAs as regulators of the endocrine system, with a focus on the identification and mode of action of several endocrine-important lncRNAs. We highlight lncRNAs that have a role in the development and function of pancreatic β cells, white and brown adipose tissue, and other endocrine organs, and discuss the involvement of these molecules in endocrine dysfunction (for example, diabetes mellitus). We also address the associations of lncRNAs with nuclear receptors involved in major hormonal signalling pathways, such as estrogen and androgen receptors, and the relevance of these associations in certain endocrine cancers.
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Affiliation(s)
- Marko Knoll
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, MA 02142, USA
| | - Harvey F Lodish
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, MA 02142, USA
| | - Lei Sun
- Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Graduate Medical School, 8 College Road, 169857, Singapore
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34
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Sun M, Kraus WL. From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev 2015; 36:25-64. [PMID: 25426780 PMCID: PMC4309736 DOI: 10.1210/er.2014-1034] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a relatively poorly understood class of RNAs with little or no coding capacity transcribed from a set of incompletely annotated genes. They have received considerable attention in the past few years and are emerging as potentially important players in biological regulation. Here we discuss the evolving understanding of this new class of molecular regulators that has emerged from ongoing research, which continues to expand our databases of annotated lncRNAs and provide new insights into their physical properties, molecular mechanisms of action, and biological functions. We outline the current strategies and approaches that have been employed to identify and characterize lncRNAs, which have been instrumental in revealing their multifaceted roles ranging from cis- to trans-regulation of gene expression and from epigenetic modulation in the nucleus to posttranscriptional control in the cytoplasm. In addition, we highlight the molecular and biological functions of some of the best characterized lncRNAs in physiology and disease, especially those relevant to endocrinology, reproduction, metabolism, immunology, neurobiology, muscle biology, and cancer. Finally, we discuss the tremendous diagnostic and therapeutic potential of lncRNAs in cancer and other diseases.
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Affiliation(s)
- Miao Sun
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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35
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Ottaviani S, de Giorgio A, Harding V, Stebbing J, Castellano L. Noncoding RNAs and the control of hormonal signaling via nuclear receptor regulation. J Mol Endocrinol 2014; 53:R61-70. [PMID: 25062739 DOI: 10.1530/jme-14-0134] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Despite its identification over 100 years ago, new discoveries continue to add to the complexity of the regulation of the endocrine system. Today the nuclear receptors (NRs) that play such a pivotal role in the extensive communication networks of hormones and gene expression remain an area of intense research. By orchestrating core processes, from metabolism to organismal development, the gene expression programs they control are dependent on their cellular context, their own levels, and those of numerous co-regulatory proteins. A previously unknown component of these networks, noncoding RNAs (ncRNAs) are now recognized as potent regulators of NR signaling, influencing receptor and co-factor levels and functions while being reciprocally regulated by the NRs themselves. This review explores the regulation enacted by microRNAs and long ncRNAs on NR function, using representative examples to show the varied roles of ncRNAs, in turn producing significant effects on the NR functional network in health and disease.
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Affiliation(s)
- Silvia Ottaviani
- Department of Surgery and CancerImperial College London, Imperial Centre for Translational and Experimental Medicine, London W12 0NN, UK
| | - Alexander de Giorgio
- Department of Surgery and CancerImperial College London, Imperial Centre for Translational and Experimental Medicine, London W12 0NN, UK
| | - Victoria Harding
- Department of Surgery and CancerImperial College London, Imperial Centre for Translational and Experimental Medicine, London W12 0NN, UK
| | - Justin Stebbing
- Department of Surgery and CancerImperial College London, Imperial Centre for Translational and Experimental Medicine, London W12 0NN, UK
| | - Leandro Castellano
- Department of Surgery and CancerImperial College London, Imperial Centre for Translational and Experimental Medicine, London W12 0NN, UK
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36
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Jiang YJ, Bikle DD. LncRNA profiling reveals new mechanism for VDR protection against skin cancer formation. J Steroid Biochem Mol Biol 2014; 144 Pt A:87-90. [PMID: 24342142 DOI: 10.1016/j.jsbmb.2013.11.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 11/05/2013] [Accepted: 11/13/2013] [Indexed: 12/13/2022]
Abstract
Accumulating evidence strongly suggests a protective role of vitamin D signaling against chemical and UVR-induced skin cancer formation. However, the mechanism remains largely unknown. Recently, the emerging role of long, non-coding RNA (lncRNA) as a hallmark of cancer has become better appreciated. LncRNAs are mRNA-like transcripts ranging in length from 200 bases to 100kb lacking significant open reading frames, which are involved in a broad spectrum of tumorigenic/metastatic processes. In this study we profiled 90 well-annotated mouse lncRNAs from cultured mouse keratinocytes after deleting the vitamin D receptor (VDR) (∼90%) vs. control cells using an lncRNA array analysis. We found that several well-known oncogenes, including H19, HOTTIP and Nespas, are significantly increased (6.3-1.8-fold), whereas tumor suppressors (Kcnq1ot1, lincRNA-p21) are decreased (up to 50-70%) in VDR deleted keratinocytes. A similar pattern of lncRNA profiling is observed in the epidermis of K14 driven, tamoxifen-regulated epidermal-specific VDR null vs. wild-type control mice. Additionally there is an increase in the expression levels of other oncogenes (mHOTAIR, Malat1 and SRA) and a decrease of other tumor suppressors (Foxn2-as, Gtl2-as, H19-as). The increased expression levels of HOTTIP and H19 were further confirmed by real-time PCR analysis with individually designed primer sets. The major finding of this study is a novel mechanism for protection by VDR against skin cancer formation by maintaining the balance of oncogenic to tumor suppressing lncRNAs. In keratinocytes lacking VDR this balance is disturbed with increased expression of oncogenes and decreased expression of tumor suppressors, a mechanism that predisposes the VDR deficient mice to skin cancer formation. This article is part of a Special Issue entitled "Vitamin D Workshop".
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Affiliation(s)
- Yan J Jiang
- Endocrine Research Unit (111N), Department of Medicine, VAMC/UCSF, NCIRE, United States.
| | - Daniel D Bikle
- Endocrine Research Unit (111N), Department of Medicine, VAMC/UCSF, NCIRE, United States
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37
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Hajjari M, Khoshnevisan A, Shin YK. Molecular function and regulation of long non-coding RNAs: paradigms with potential roles in cancer. Tumour Biol 2014; 35:10645-63. [PMID: 25266799 DOI: 10.1007/s13277-014-2636-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/12/2014] [Indexed: 01/06/2023] Open
Abstract
Different long non-coding RNAs (lncRNAs) are transcribed within the genome. Although initially argued to be spurious transcriptional noise, these RNAs play important roles in biological pathways, as shown by different studies. Also, there are some reports about the role of lncRNAs in different cancers. They can contribute to the development and progression of cancer by the functioning as oncogene or/and tumor suppressor molecules. In this review, we point to some important lncRNAs as examples which seem to be involved in cancer initiation/progression.
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38
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O'Neill DJ, Williamson SC, Alkharaif D, Monteiro ICM, Goudreault M, Gaughan L, Robson CN, Gingras AC, Binda O. SETD6 controls the expression of estrogen-responsive genes and proliferation of breast carcinoma cells. Epigenetics 2014; 9:942-50. [PMID: 24751716 PMCID: PMC4143409 DOI: 10.4161/epi.28864] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 12/24/2022] Open
Abstract
The lysine methyltransferase SETD6 modifies the histone variant H2AZ, a key component of nuclear receptor-dependent transcription. Herein, we report the identification of several factors that associate with SETD6 and are implicated in nuclear hormone receptor signaling. Specifically, SETD6 associates with the estrogen receptor α (ERα), histone deacetylase HDAC1, metastasis protein MTA2, and the transcriptional co-activator TRRAP. Luciferase reporter assays identify SETD6 as a transcriptional repressor, in agreement with its association with HDAC1 and MTA2. However, SETD6 behaves as a co-activator of several estrogen-responsive genes, such as PGR and TFF1. Consistent with these results, silencing of SETD6 in several breast carcinoma cell lines induced cellular proliferation defects accompanied by enhanced expression of the cell cycle inhibitor CDKN1A and induction of apoptosis. Herein, we have identified several chromatin proteins that associate with SETD6 and described SETD6 as an essential factor for nuclear receptor signaling and cellular proliferation.
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Affiliation(s)
- Daniel J O'Neill
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | | | - Dhuha Alkharaif
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | | | - Marilyn Goudreault
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto, ON Canada
| | - Luke Gaughan
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | - Craig N Robson
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto, ON Canada
- Department of Molecular Genetics; University of Toronto; Toronto, ON Canada
| | - Olivier Binda
- Northern Institute for Cancer Research; Newcastle University; Newcastle upon Tyne, UK
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39
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Arieti F, Gabus C, Tambalo M, Huet T, Round A, Thore S. The crystal structure of the Split End protein SHARP adds a new layer of complexity to proteins containing RNA recognition motifs. Nucleic Acids Res 2014; 42:6742-52. [PMID: 24748666 PMCID: PMC4041450 DOI: 10.1093/nar/gku277] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The Split Ends (SPEN) protein was originally discovered in Drosophila in the late 1990s. Since then, homologous proteins have been identified in eukaryotic species ranging from plants to humans. Every family member contains three predicted RNA recognition motifs (RRMs) in the N-terminal region of the protein. We have determined the crystal structure of the region of the human SPEN homolog that contains these RRMs—the SMRT/HDAC1 Associated Repressor Protein (SHARP), at 2.0 Å resolution. SHARP is a co-regulator of the nuclear receptors. We demonstrate that two of the three RRMs, namely RRM3 and RRM4, interact via a highly conserved interface. Furthermore, we show that the RRM3–RRM4 block is the main platform mediating the stable association with the H12–H13 substructure found in the steroid receptor RNA activator (SRA), a long, non-coding RNA previously shown to play a crucial role in nuclear receptor transcriptional regulation. We determine that SHARP association with SRA relies on both single- and double-stranded RNA sequences. The crystal structure of the SHARP–RRM fragment, together with the associated RNA-binding studies, extend the repertoire of nucleic acid binding properties of RRM domains suggesting a new hypothesis for a better understanding of SPEN protein functions.
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Affiliation(s)
- Fabiana Arieti
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Caroline Gabus
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Margherita Tambalo
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Tiphaine Huet
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation and Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, Grenoble 38042, France
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
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40
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Jiang YJ, Bikle DD. LncRNA: a new player in 1α, 25(OH)(2) vitamin D(3) /VDR protection against skin cancer formation. Exp Dermatol 2014; 23:147-50. [PMID: 24499465 PMCID: PMC4103949 DOI: 10.1111/exd.12341] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2014] [Indexed: 12/12/2022]
Abstract
Sunlight, vitamin D and skin cancer form a controversial brew. While too much sunlight exposure causes skin cancer, it is the major source of vitamin D from skin. We propose that these processes can be balanced. Vitamin D signalling (VDS) protects against skin cancer as demonstrated by the susceptibility of the skin to tumor formation in VDR null mice and protection from UVB-induced mutations when VDR agonists are administered. The question is how is protection afforded. Previously, we have focused on the Wnt/β-catenin/hedgehog and DNA damage repair (DDR) pathways. As VDR regulates hundreds of genes with thousands of VDR response elements (VDRE) throughout the genome, and many VDREs are in non-coding regions, we decided to explore long non-coding RNAs (lncRNA). LncRNAs are mRNA-like transcripts ranging from 200 bases ~100 kb lacking significant open reading frames. They are aberrantly expressed in human cancers and involved in a spectrum of tumorigenic/metastatic processes (cell proliferation/apoptosis/angiogenesis). We discovered that VDS regulated the expression of certain lncRNAs in a manner consistent with VDS protection against skin cancer. Given the huge variation in genes actively regulated by 1,25(OH)2 D from different cell types, it is conceivable that our results could apply to personalized medicine based on the distinctive lncRNA profiles. These lncRNAs could also serve as skin cancer biomarkers secreted into the blood or urine via exosomes as demonstrated in other cancer types (breast, prostate). Modulation of lncRNA profile by VDS may also provide insight into regulating pathways such as Wnt/ß-catenin and hedgehog.
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Affiliation(s)
- Yan J Jiang
- Endocrine Research Unit (111N), Department of Medicine, VAMC/UCSF, NCIRE, San Francisco, CA, USA
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41
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Johnsson P, Lipovich L, Grandér D, Morris KV. Evolutionary conservation of long non-coding RNAs; sequence, structure, function. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1840:1063-71. [PMID: 24184936 PMCID: PMC3909678 DOI: 10.1016/j.bbagen.2013.10.035] [Citation(s) in RCA: 498] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 10/15/2013] [Accepted: 10/21/2013] [Indexed: 12/31/2022]
Abstract
BACKGROUND Recent advances in genomewide studies have revealed the abundance of long non-coding RNAs (lncRNAs) in mammalian transcriptomes. The ENCODE Consortium has elucidated the prevalence of human lncRNA genes, which are as numerous as protein-coding genes. Surprisingly, many lncRNAs do not show the same pattern of high interspecies conservation as protein-coding genes. The absence of functional studies and the frequent lack of sequence conservation therefore make functional interpretation of these newly discovered transcripts challenging. Many investigators have suggested the presence and importance of secondary structural elements within lncRNAs, but mammalian lncRNA secondary structure remains poorly understood. It is intriguing to speculate that in this group of genes, RNA secondary structures might be preserved throughout evolution and that this might explain the lack of sequence conservation among many lncRNAs. SCOPE OF REVIEW Here, we review the extent of interspecies conservation among different lncRNAs, with a focus on a subset of lncRNAs that have been functionally investigated. The function of lncRNAs is widespread and we investigate whether different forms of functionalities may be conserved. MAJOR CONCLUSIONS Lack of conservation does not imbue a lack of function. We highlight several examples of lncRNAs where RNA structure appears to be the main functional unit and evolutionary constraint. We survey existing genomewide studies of mammalian lncRNA conservation and summarize their limitations. We further review specific human lncRNAs which lack evolutionary conservation beyond primates but have proven to be both functional and therapeutically relevant. GENERAL SIGNIFICANCE Pioneering studies highlight a role in lncRNAs for secondary structures, and possibly the presence of functional "modules", which are interspersed with longer and less conserved stretches of nucleotide sequences. Taken together, high-throughput analysis of conservation and functional composition of the still-mysterious lncRNA genes is only now becoming feasible.
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Affiliation(s)
- Per Johnsson
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA; Department of Neurology, Wayne State University School of Medicine, Detriot, MI, USA
| | - Dan Grandér
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Kevin V Morris
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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42
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McKay DB, Xi L, Barthel KKB, Cech TR. Structure and function of steroid receptor RNA activator protein, the proposed partner of SRA noncoding RNA. J Mol Biol 2014; 426:1766-1785. [PMID: 24486609 DOI: 10.1016/j.jmb.2014.01.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/21/2014] [Accepted: 01/22/2014] [Indexed: 11/28/2022]
Abstract
In a widely accepted model, the steroid receptor RNA activator protein (SRA protein; SRAP) modulates the transcriptional regulatory activity of SRA RNA by binding a specific stem-loop of SRA. We first confirmed that SRAP is present in the nucleus as well as the cytoplasm of MCF-7 breast cancer cells, where it is expressed at the level of about 10(5) molecules per cell. However, our SRAP-RNA binding experiments, both in vitro with recombinant protein and in cultured cells with plasmid-expressed protein and RNA, did not reveal a specific interaction between SRAP and SRA. We determined the crystal structure of the carboxy-terminal domain of human SRAP and found that it does not have the postulated RRM (RNA recognition motif). The structure is a five-helix bundle that is distinct from known RNA-binding motifs and instead is similar to the carboxy-terminal domain of the yeast spliceosome protein PRP18, which stabilizes specific protein-protein interactions within a multisubunit mRNA splicing complex. SRA binding experiments with this domain gave negative results. Transcriptional regulation by SRA/SRAP was examined with siRNA knockdown. Effects on both specific estrogen-responsive genes and genes identified by RNA-seq as candidates for regulation were examined in MCF-7 cells. Only a small effect (~20% change) on one gene resulting from depletion of SRA/SRAP could be confirmed. We conclude that the current model for SRAP function must be reevaluated; we suggest that SRAP may function in a different context to stabilize specific intermolecular interactions in the nucleus.
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Affiliation(s)
- David B McKay
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA.,Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.,Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Linghe Xi
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Kristen K B Barthel
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Thomas R Cech
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA.,Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.,Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
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43
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Bilinovich SM, Davis CM, Morris DL, Ray LA, Prokop JW, Buchan GJ, Leeper TC. The C-terminal domain of SRA1p has a fold more similar to PRP18 than to an RRM and does not directly bind to the SRA1 RNA STR7 region. J Mol Biol 2014; 426:1753-65. [PMID: 24486611 DOI: 10.1016/j.jmb.2014.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/14/2014] [Accepted: 01/16/2014] [Indexed: 12/23/2022]
Abstract
Steroid receptor activator RNA protein (SRA1p) is the translation product of the bi-functional long non-coding RNA steroid receptor activator RNA 1 (SRA1) that is part of the steroid receptor coactivator-1 acetyltransferase complex and is indicated to be an epigenetic regulatory component. Previously, the SRA1p protein was suggested to contain an RNA recognition motif (RRM) domain. We have determined the solution structure of the C-terminal domain of human SRA1p by NMR spectroscopy. Our structure along with sequence comparisons among SRA1p orthologs and against authentic RRM proteins indicates that it is not an RRM domain but rather an all-helical protein with a fold more similar to the PRP18 splicing factor. NMR spectroscopy on the full SRA1p protein suggests that this structure is relevant to the native full-length context. Furthermore, molecular modeling indicates that this fold is well conserved among vertebrates. Amino acid variations in this protein seen across sequenced human genomes, including those in tumor cells, indicate that mutations that disrupt the fold occur vary rarely and highlight that its function is well conserved. SRA1p had previously been suggested to bind to the SRA1 RNA, but NMR spectra of SRA1p in the presence of its 80-nt RNA target suggest otherwise and indicate that this protein must be part of a multi-protein complex in order to recognize its proposed RNA recognition element.
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Affiliation(s)
| | - Caroline M Davis
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA
| | - Daniel L Morris
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA
| | - Louis A Ray
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA
| | - Jeremy W Prokop
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Gregory J Buchan
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA
| | - Thomas C Leeper
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA.
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44
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Kugel JF, Goodrich JA. The regulation of mammalian mRNA transcription by lncRNAs: recent discoveries and current concepts. Epigenomics 2013; 5:95-102. [PMID: 23414324 DOI: 10.2217/epi.12.69] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Transcription by RNA Pol II is a tightly controlled process that is critical to normal cellular metabolism. Understanding how transcriptional regulation is orchestrated has mainly involved identifying and characterizing proteins that function as transcription factors. During the past decade, however, an increasing number of lncRNAs have been identified as transcriptional regulators. This revelation has spurred new discoveries, novel techniques and paradigm shifts, which together are redefining our understanding of transcriptional control and broadening our view of RNA function. Here, we summarize recent discoveries concerning the role of lncRNAs as regulators of mammalian mRNA transcription, with a focus on key concepts that are guiding current research in the field.
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Affiliation(s)
- Jennifer F Kugel
- Department of Chemistry & Biochemistry, University of Colorado, 596 UCB, Boulder, CO 80309-0596, USA
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45
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Colley SM, Wintle L, Searles R, Russell V, Firman RC, Smith S, DeBoer K, Merriner DJ, Genevieve B, Bentel JM, Stuckey BGA, Phillips MR, Simmons LW, de Kretser DM, O'Bryan MK, Leedman PJ. Loss of the nuclear receptor corepressor SLIRP compromises male fertility. PLoS One 2013; 8:e70700. [PMID: 23976951 PMCID: PMC3744554 DOI: 10.1371/journal.pone.0070700] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/20/2013] [Indexed: 11/24/2022] Open
Abstract
Nuclear receptors (NRs) and their coregulators play fundamental roles in initiating and directing gene expression influencing mammalian reproduction, development and metabolism. SRA stem Loop Interacting RNA-binding Protein (SLIRP) is a Steroid receptor RNA Activator (SRA) RNA-binding protein that is a potent repressor of NR activity. SLIRP is present in complexes associated with NR target genes in the nucleus; however, it is also abundant in mitochondria where it affects mitochondrial mRNA transcription and energy turnover. In further characterisation studies, we observed SLIRP protein in the testis where its localization pattern changes from mitochondrial in diploid cells to peri-acrosomal and the tail in mature sperm. To investigate the in vivo effects of SLIRP, we generated a SLIRP knockout (KO) mouse. This animal is viable, but sub-fertile. Specifically, when homozygous KO males are crossed with wild type (WT) females the resultant average litter size is reduced by approximately one third compared with those produced by WT males and females. Further, SLIRP KO mice produced significantly fewer progressively motile sperm than WT animals. Electron microscopy identified disruption of the mid-piece/annulus junction in homozygous KO sperm and altered mitochondrial morphology. In sum, our data implicates SLIRP in regulating male fertility, wherein its loss results in asthenozoospermia associated with compromised sperm structure and mitochondrial morphology.
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Affiliation(s)
- Shane M. Colley
- Laboratory for Cancer Medicine, The University of Western Australia Centre for Medical Research, Western Australian Institute for Medical Research, Perth, Australia
| | - Larissa Wintle
- Laboratory for Cancer Medicine, The University of Western Australia Centre for Medical Research, Western Australian Institute for Medical Research, Perth, Australia
| | | | - Victoria Russell
- Laboratory for Cancer Medicine, The University of Western Australia Centre for Medical Research, Western Australian Institute for Medical Research, Perth, Australia
| | - Renee C. Firman
- Centre for Evolutionary Biology, School of Animal Biology, The University of Western Australia, Crawley, Australia
| | - Stephanie Smith
- Male Infertility and Germ Cell Biology Laboratory, Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - Kathleen DeBoer
- Male Infertility and Germ Cell Biology Laboratory, Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - D. Jo Merriner
- Male Infertility and Germ Cell Biology Laboratory, Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - Ben Genevieve
- Keogh Institute for Medical Research, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Jacqueline M. Bentel
- Anatomical Pathology, PathWest Laboratory Medicine, Royal Perth Hospital, Perth, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Australia
| | - Bronwyn G. A. Stuckey
- Keogh Institute for Medical Research, Sir Charles Gairdner Hospital, Nedlands, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley, Australia
| | - Michael R. Phillips
- Laboratory for Cancer Medicine, The University of Western Australia Centre for Medical Research, Western Australian Institute for Medical Research, Perth, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley, Australia
| | - Leigh W. Simmons
- Centre for Evolutionary Biology, School of Animal Biology, The University of Western Australia, Crawley, Australia
| | - David M. de Kretser
- Male Infertility and Germ Cell Biology Laboratory, Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - Moira K. O'Bryan
- Male Infertility and Germ Cell Biology Laboratory, Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - Peter J. Leedman
- Laboratory for Cancer Medicine, The University of Western Australia Centre for Medical Research, Western Australian Institute for Medical Research, Perth, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley, Australia
- * E-mail:
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46
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Sun M, Kraus WL. Minireview: Long noncoding RNAs: new "links" between gene expression and cellular outcomes in endocrinology. Mol Endocrinol 2013; 27:1390-402. [PMID: 23885095 DOI: 10.1210/me.2013-1113] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Recent advances in sequencing technologies have revealed that the genome is extensively transcribed, yielding a large repertoire of noncoding RNAs. These include long noncoding RNAs (lncRNAs), mRNA-like molecules that do not code for proteins, which are emerging as a new class of RNAs that play important roles in a variety of cellular processes. Ongoing studies are revealing new insights about lncRNAs, including their physiological functions, disease relationships, and molecular mechanisms of action. Characterized lncRNAs have been shown to interact with and modulate the activity of other RNAs and protein partners, leading to alterations in transcriptional and posttranscriptional regulatory processes. In this review, we summarize the key features of lncRNAs, their molecular mechanisms of action, biological functions, and therapeutic implications, particularly as they apply to the field of molecular endocrinology. In addition, we provide a brief overview of how molecular biologists are beginning to probe the identity, mechanisms, and functions of this emerging class of RNA molecules.
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Affiliation(s)
- Miao Sun
- Department of Molecular Biology and Genetics and Graduate Field of Biochemistry, Cornell University, Ithaca, New York 14853, USA
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47
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Vicent GP, Nacht AS, Zaurin R, Font-Mateu J, Soronellas D, Le Dily F, Reyes D, Beato M. Unliganded progesterone receptor-mediated targeting of an RNA-containing repressive complex silences a subset of hormone-inducible genes. Genes Dev 2013; 27:1179-97. [PMID: 23699411 DOI: 10.1101/gad.215293.113] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A close chromatin conformation precludes gene expression in eukaryotic cells. Genes activated by external cues have to overcome this repressive state by locally changing chromatin structure to a more open state. Although much is known about hormonal gene activation, how basal repression of regulated genes is targeted to the correct sites throughout the genome is not well understood. Here we report that in breast cancer cells, the unliganded progesterone receptor (PR) binds genomic sites and targets a repressive complex containing HP1γ (heterochromatin protein 1γ), LSD1 (lysine-specific demethylase 1), HDAC1/2, CoREST (corepressor for REST [RE1 {neuronal repressor element 1} silencing transcription factor]), KDM5B, and the RNA SRA (steroid receptor RNA activator) to 20% of hormone-inducible genes, keeping these genes silenced prior to hormone treatment. The complex is anchored via binding of HP1γ to H3K9me3 (histone H3 tails trimethylated on Lys 9). SRA interacts with PR, HP1γ, and LSD1, and its depletion compromises the loading of the repressive complex to target chromatin-promoting aberrant gene derepression. Upon hormonal treatment, the HP1γ-LSD1 complex is displaced from these constitutively poorly expressed genes as a result of rapid phosphorylation of histone H3 at Ser 10 mediated by MSK1, which is recruited to the target sites by the activated PR. Displacement of the repressive complex enables the loading of coactivators needed for chromatin remodeling and activation of this set of genes, including genes involved in apoptosis and cell proliferation. These results highlight the importance of the unliganded PR in hormonal regulation of breast cancer cells.
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48
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Beato M, Vicent GP. A new role for an old player: steroid receptor RNA Activator (SRA) represses hormone inducible genes. Transcription 2013; 4:167-71. [PMID: 23863201 DOI: 10.4161/trns.25777] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In breast cancer cells the Steroid Receptor ¬RNA Activator (SRA) acts as scaffold of a complex containing HP1γ, LSD1, HDAC1/2 and CoREST, which contributes to repression of key hormone-inducible genes that must be kept silent in the absence of hormone.
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49
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Regulatory Roles for Long ncRNA and mRNA. Cancers (Basel) 2013; 5:462-90. [PMID: 24216986 PMCID: PMC3730338 DOI: 10.3390/cancers5020462] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/05/2013] [Accepted: 04/19/2013] [Indexed: 01/31/2023] Open
Abstract
Recent advances in high-throughput sequencing technology have identified the transcription of a much larger portion of the genome than previously anticipated. Especially in the context of cancer it has become clear that aberrant transcription of both protein-coding and long non-coding RNAs (lncRNAs) are frequent events. The current dogma of RNA function describes mRNA to be responsible for the synthesis of proteins, whereas non-coding RNA can have regulatory or epigenetic functions. However, this distinction between protein coding and regulatory ability of transcripts may not be that strict. Here, we review the increasing body of evidence for the existence of multifunctional RNAs that have both protein-coding and trans-regulatory roles. Moreover, we demonstrate that coding transcripts bind to components of the Polycomb Repressor Complex 2 (PRC2) with similar affinities as non-coding transcripts, revealing potential epigenetic regulation by mRNAs. We hypothesize that studies on the regulatory ability of disease-associated mRNAs will form an important new field of research.
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50
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Lightowlers RN, Chrzanowska-Lightowlers ZMA. Human pentatricopeptide proteins: only a few and what do they do? RNA Biol 2013; 10:1433-8. [PMID: 23635806 PMCID: PMC3858426 DOI: 10.4161/rna.24770] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins constitute a large family of RNA-binding proteins that contain a canonical 35 residue repeat motif. Originally identified in Arabidopsis thaliana, family members are found in protists, fungi, and metazoan but are by far most abundant in plant organelles. Seven examples have been identified in human mitochondria and roles have been tentatively ascribed to each. In this review, we briefly outline each of these PPR proteins and discuss the role each is believed to play in facilitating mitochondrial gene expression.
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Affiliation(s)
- Robert N Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research; Institute for Cell and Molecular Biosciences; Newcastle University; The Medical School; Framlington Place; Newcastle upon Tyne, UK
| | - Zofia M A Chrzanowska-Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research; Institute for Ageing and Health; Newcastle University; The Medical School; Framlington Place; Newcastle upon Tyne, UK
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