1
|
Barlit H, Romero AM, Gülhan A, Patnaik PK, Tyshkovskiy A, Martínez-Pastor MT, Gladyshev VN, Puig S, Labunskyy VM. Ribosome profiling reveals the role of yeast RNA-binding proteins Cth1 and Cth2 in translational regulation. iScience 2024; 27:109868. [PMID: 38779483 PMCID: PMC11109004 DOI: 10.1016/j.isci.2024.109868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/12/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Iron serves as a cofactor for enzymes involved in several steps of protein translation, but the control of translation during iron limitation is not understood at the molecular level. Here, we report a genome-wide analysis of protein translation in response to iron deficiency in yeast using ribosome profiling. We show that iron depletion affects global protein synthesis and leads to translational repression of multiple genes involved in iron-related processes. Furthermore, we demonstrate that the RNA-binding proteins Cth1 and Cth2 play a central role in this translational regulation by repressing the activity of the iron-dependent Rli1 ribosome recycling factor and inhibiting mitochondrial translation and heme biosynthesis. Additionally, we found that iron deficiency represses MRS3 mRNA translation through increased expression of antisense long non-coding RNA. Together, our results reveal complex gene expression and protein synthesis remodeling in response to low iron, demonstrating how this important metal affects protein translation at multiple levels.
Collapse
Affiliation(s)
- Hanna Barlit
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Antonia M. Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Ali Gülhan
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Praveen K. Patnaik
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - María T. Martínez-Pastor
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Valencia, Spain
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Vyacheslav M. Labunskyy
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| |
Collapse
|
2
|
He D, Mount SM, Patro R. scCensus: Off-target scRNA-seq reads reveal meaningful biology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577807. [PMID: 38352549 PMCID: PMC10862729 DOI: 10.1101/2024.01.29.577807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Single-cell RNA-sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity. Although scRNA-seq reads from most prevalent and popular tagged-end protocols are expected to arise from the 3' end of polyadenylated RNAs, recent studies have shown that "off-target" reads can constitute a substantial portion of the read population. In this work, we introduced scCensus, a comprehensive analysis workflow for systematically evaluating and categorizing off-target reads in scRNA-seq. We applied scCensus to seven scRNA-seq datasets. Our analysis of intergenic reads shows that these off-target reads contain information about chromatin structure and can be used to identify similar cells across modalities. Our analysis of antisense reads suggests that these reads can be used to improve gene detection and capture interesting transcriptional activities like antisense transcription. Furthermore, using splice-aware quantification, we find that spliced and unspliced reads provide distinct information about cell clusters and biomarkers, suggesting the utility of integrating signals from reads with different splicing statuses. Overall, our results suggest that off-target scRNA-seq reads contain underappreciated information about various transcriptional activities. These observations about yet-unexploited information in existing scRNA-seq data will help guide and motivate the community to improve current algorithms and analysis methods, and to develop novel approaches that utilize off-target reads to extend the reach and accuracy of single-cell data analysis pipelines.
Collapse
Affiliation(s)
- Dongze He
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
- Program in Computational Biology, Bioinformatics and Genomices, University of Maryland, College Park, MD 20742, USA
| | - Stephen M. Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Rob Patro
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
3
|
Grandchamp A, Czuppon P, Bornberg-Bauer E. Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster. Nucleic Acids Res 2024; 52:274-287. [PMID: 38000384 PMCID: PMC10783523 DOI: 10.1093/nar/gkad1079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/13/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
Most of the transcribed eukaryotic genomes are composed of non-coding transcripts. Among these transcripts, some are newly transcribed when compared to outgroups and are referred to as de novo transcripts. De novo transcripts have been shown to play a major role in genomic innovations. However, little is known about the rates at which de novo transcripts are gained and lost in individuals of the same species. Here, we address this gap and estimate the de novo transcript turnover rate with an evolutionary model. We use DNA long reads and RNA short reads from seven geographically remote samples of inbred individuals of Drosophila melanogaster to detect de novo transcripts that are gained on a short evolutionary time scale. Overall, each sampled individual contains around 2500 unspliced de novo transcripts, with most of them being sample specific. We estimate that around 0.15 transcripts are gained per year, and that each gained transcript is lost at a rate around 5× 10-5 per year. This high turnover of transcripts suggests frequent exploration of new genomic sequences within species. These rate estimates are essential to comprehend the process and timescale of de novo gene birth.
Collapse
Affiliation(s)
- Anna Grandchamp
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Peter Czuppon
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| |
Collapse
|
4
|
Du J, Su Y, Gao J, Tai Y. The expression and function of long noncoding RNAs in hepatocellular carcinoma. CANCER INNOVATION 2023; 2:488-499. [PMID: 38125766 PMCID: PMC10730004 DOI: 10.1002/cai2.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 12/23/2023]
Abstract
With the deepening of the genome project study, attention on noncoding RNAs is increasing. Long noncoding RNAs (lncRNAs) have become a new research hotspot. A growing number of studies have revealed that lncRNAs are involved in tumorigenesis and tumor suppressor pathways. Aberrant expressions of lncRNAs have been found in a variety of human tumors including hepatocellular carcinoma (HCC). In this review, we provide a brief introduction to lncRNA and highlight recent research on the functions and clinical significance of lncRNAs in HCC.
Collapse
Affiliation(s)
- Jingli Du
- Senior Department of TuberculosisThe 8th Medical Center of PLA General HospitalBeijingChina
| | - Yue Su
- Senior Department of TuberculosisThe 8th Medical Center of PLA General HospitalBeijingChina
| | - Jianzhi Gao
- Department of OncologyZhuozhou Hospital, ZhuozhouHebeiChina
| | - Yanhong Tai
- Department of PathologyThe 5th Medical Center of PLA General HospitalBeijingChina
| |
Collapse
|
5
|
Interdependent Transcription of a Natural Sense/Antisense Transcripts Pair (SLC34A1/PFN3). Noncoding RNA 2022; 8:ncrna8010019. [PMID: 35202092 PMCID: PMC8877773 DOI: 10.3390/ncrna8010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Natural antisense transcripts (NATs) constitute a significant group of regulatory, long noncoding RNAs. They are prominently expressed in testis but are also detectable in other organs. NATs are transcribed at low levels and co-expressed with related protein coding sense transcripts. Nowadays NATs are generally considered as regulatory, long noncoding RNAs without closer focus on the inevitable interference between sense and antisense expression. This work describes a cellular system where sense and antisense transcription of a specific locus (SLC34A1/PFN3) is induced using epigenetic modifiers and CRISPR-Cas9. The renal cell lines HEK293 and HKC-8 do not express SLC34A1/PFN3 under normal culture conditions. Five-day exposure to dexamethasone significantly stimulates sense transcript (SLC34A1) levels and antisense (PFN3) minimally; the effect is only seen in HEK293 cells. Enhanced expression is paralleled by reduced sense promoter methylation and an increase in activating histone marks. Expression is further modulated by cassettes that stimulate the expression of sense or antisense transcript but disrupt protein coding potential. Constitutive expression of a 5′-truncated SLC34A1 transcript increases sense expression independent of dexamethasone induction but also stimulates antisense expression. Concordant expression is confirmed with the antisense knock-in that also enhances sense expression. The antisense effect acts on transcription in cis since transient transfection with sense or antisense constructs fails to stimulate the expression of the opposite transcript. These results suggest that bi-directional transcription of the SLC34A1/PFN3 locus has a stimulatory influence on the expression of the opposite transcript involving epigenetic changes of the promoters. In perspective of extensive, previous research into bi-directionally transcribed SLC34A loci, the findings underpin a hypothesis where NATs display different biological roles in soma and germ cells. Accordingly, we propose that in somatic cells, NATs act like lncRNAs–with the benefit of close proximity to a potential target gene. In germ cells, however, recent evidence suggests different biological roles for NATs that require RNA complementarity and double-stranded RNA formation.
Collapse
|
6
|
Irfan J, Febrianto MR, Sharma A, Rose T, Mahmudzade Y, Di Giovanni S, Nagy I, Torres-Perez JV. DNA Methylation and Non-Coding RNAs during Tissue-Injury Associated Pain. Int J Mol Sci 2022; 23:ijms23020752. [PMID: 35054943 PMCID: PMC8775747 DOI: 10.3390/ijms23020752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
While about half of the population experience persistent pain associated with tissue damages during their lifetime, current symptom-based approaches often fail to reduce such pain to a satisfactory level. To provide better patient care, mechanism-based analgesic approaches must be developed, which necessitates a comprehensive understanding of the nociceptive mechanism leading to tissue injury-associated persistent pain. Epigenetic events leading the altered transcription in the nervous system are pivotal in the maintenance of pain in tissue injury. However, the mechanisms through which those events contribute to the persistence of pain are not fully understood. This review provides a summary and critical evaluation of two epigenetic mechanisms, DNA methylation and non-coding RNA expression, on transcriptional modulation in nociceptive pathways during the development of tissue injury-associated pain. We assess the pre-clinical data and their translational implication and evaluate the potential of controlling DNA methylation and non-coding RNA expression as novel analgesic approaches and/or biomarkers of persistent pain.
Collapse
Affiliation(s)
- Jahanzaib Irfan
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Muhammad Rizki Febrianto
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Anju Sharma
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Thomas Rose
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Yasamin Mahmudzade
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
| | - Simone Di Giovanni
- Department of Brain Sciences, Division of Neuroscience, Imperial College London, E505, Burlington Danes, Du Cane Road, London W12 ONN, UK;
| | - Istvan Nagy
- Nociception Group, Department of Surgery and Cancer, Division of Anaesthetics, Pain Medicine and Intensive Care, Chelsea and Westminster Hospital Campus, Imperial College London, 369 Fulham Road, London SW10 9FJ, UK; (J.I.); (M.R.F.); (A.S.); (T.R.); (Y.M.)
- Correspondence: (I.N.); (J.V.T.-P.)
| | - Jose Vicente Torres-Perez
- Department of Brain Sciences, Dementia Research Institute, Imperial College London, 86 Wood Ln, London W12 0BZ, UK
- Departament de Biologia Cellular, Biologia Funcional i Antropologia Física, Facultat de Ciències Biològiques, Universitat de València, C/Dr. Moliner 50, 46100 Burjassot, Spain
- Correspondence: (I.N.); (J.V.T.-P.)
| |
Collapse
|
7
|
Srinivasan C, Phan BN, Lawler AJ, Ramamurthy E, Kleyman M, Brown AR, Kaplow IM, Wirthlin ME, Pfenning AR. Addiction-Associated Genetic Variants Implicate Brain Cell Type- and Region-Specific Cis-Regulatory Elements in Addiction Neurobiology. J Neurosci 2021; 41:9008-9030. [PMID: 34462306 PMCID: PMC8549541 DOI: 10.1523/jneurosci.2534-20.2021] [Citation(s) in RCA: 8] [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: 09/28/2020] [Revised: 06/18/2021] [Accepted: 07/10/2021] [Indexed: 12/14/2022] Open
Abstract
Recent large genome-wide association studies have identified multiple confident risk loci linked to addiction-associated behavioral traits. Most genetic variants linked to addiction-associated traits lie in noncoding regions of the genome, likely disrupting cis-regulatory element (CRE) function. CREs tend to be highly cell type-specific and may contribute to the functional development of the neural circuits underlying addiction. Yet, a systematic approach for predicting the impact of risk variants on the CREs of specific cell populations is lacking. To dissect the cell types and brain regions underlying addiction-associated traits, we applied stratified linkage disequilibrium score regression to compare genome-wide association studies to genomic regions collected from human and mouse assays for open chromatin, which is associated with CRE activity. We found enrichment of addiction-associated variants in putative CREs marked by open chromatin in neuronal (NeuN+) nuclei collected from multiple prefrontal cortical areas and striatal regions known to play major roles in reward and addiction. To further dissect the cell type-specific basis of addiction-associated traits, we also identified enrichments in human orthologs of open chromatin regions of female and male mouse neuronal subtypes: cortical excitatory, D1, D2, and PV. Last, we developed machine learning models to predict mouse cell type-specific open chromatin, enabling us to further categorize human NeuN+ open chromatin regions into cortical excitatory or striatal D1 and D2 neurons and predict the functional impact of addiction-associated genetic variants. Our results suggest that different neuronal subtypes within the reward system play distinct roles in the variety of traits that contribute to addiction.SIGNIFICANCE STATEMENT We combine statistical genetic and machine learning techniques to find that the predisposition to for nicotine, alcohol, and cannabis use behaviors can be partially explained by genetic variants in conserved regulatory elements within specific brain regions and neuronal subtypes of the reward system. Our computational framework can flexibly integrate open chromatin data across species to screen for putative causal variants in a cell type- and tissue-specific manner for numerous complex traits.
Collapse
Affiliation(s)
- Chaitanya Srinivasan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - BaDoi N Phan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Medical Scientist Training Program, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Alyssa J Lawler
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Easwaran Ramamurthy
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Michael Kleyman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Ashley R Brown
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Irene M Kaplow
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Morgan E Wirthlin
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Andreas R Pfenning
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| |
Collapse
|
8
|
Najari Hanjani P, Golalipour M. Circadian Oscillation of Natural Antisense Transcripts Related to Human Core Clock Genes. Rep Biochem Mol Biol 2021; 10:471-476. [PMID: 34981025 PMCID: PMC8718779 DOI: 10.52547/rbmb.10.3.471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/06/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Circadian clocks are autonomous intracellular oscillators that synchronize metabolic and physiological processes with the external signals. So, misalignment of environmental and endogenous circadian rhythms leads to disruption of biological activities in living organisms. Noncoding transcripts including antisense RNAs are an important component of the molecular clocks. Commonly, the antisense transcripts are involved in the regulation of gene expression. PER2AS and CRY1AS are the only known Natural Antisense Transcripts (NAT) among the core clock genes, which overlap with the PER2 and CRY1 genes, respectively. In this study, we hypothesized that PER2AS and CRY1AS like the other clock genes, exhibit the oscillatory behavior in a 24-hour period and affect the expression of PER2 and CRY1. METHODS First, the A549 cell line was cultured under standard conditions. After horse serum shock, RNA extraction and cDNA synthesis was performed; then the expression fluctuations of PER2AS, CRY1AS, PER2, and CRY1 were measured with Real-time PCR. RESULTS Our result showed that PER2AS and CRY1AS had similar oscillation patterns with their sense strand during 24-hour period. CONCLUSION Therefore, we suggested that PER2AS and CRY1AS transcripts probably by preventing the interaction of miRNAs with PER2 and CRY1 mRNAs, influence the expression of them, positively.
Collapse
Affiliation(s)
| | - Masoud Golalipour
- Cellular and Molecular Research center, Golestan university of medical sciences, Gorgan, Iran.
- Golestan University of Medical Sciences, Gorgan, Iran.
| |
Collapse
|
9
|
Krappinger JC, Bonstingl L, Pansy K, Sallinger K, Wreglesworth NI, Grinninger L, Deutsch A, El-Heliebi A, Kroneis T, Mcfarlane RJ, Sensen CW, Feichtinger J. Non-coding Natural Antisense Transcripts: Analysis and Application. J Biotechnol 2021; 340:75-101. [PMID: 34371054 DOI: 10.1016/j.jbiotec.2021.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/30/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Non-coding natural antisense transcripts (ncNATs) are regulatory RNA sequences that are transcribed in the opposite direction to protein-coding or non-coding transcripts. These transcripts are implicated in a broad variety of biological and pathological processes, including tumorigenesis and oncogenic progression. With this complex field still in its infancy, annotations, expression profiling and functional characterisations of ncNATs are far less comprehensive than those for protein-coding genes, pointing out substantial gaps in the analysis and characterisation of these regulatory transcripts. In this review, we discuss ncNATs from an analysis perspective, in particular regarding the use of high-throughput sequencing strategies, such as RNA-sequencing, and summarize the unique challenges of investigating the antisense transcriptome. Finally, we elaborate on their potential as biomarkers and future targets for treatment, focusing on cancer.
Collapse
Affiliation(s)
- Julian C Krappinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Lilli Bonstingl
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Katrin Pansy
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Katja Sallinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Nick I Wreglesworth
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Lukas Grinninger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Austrian Biotech University of Applied Sciences, Konrad Lorenz-Straße 10, 3430 Tulln an der Donau, Austria
| | - Alexander Deutsch
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Amin El-Heliebi
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Thomas Kroneis
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Ramsay J Mcfarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Christoph W Sensen
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria; Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; HCEMM Kft., Római blvd. 21, 6723 Szeged, Hungary
| | - Julia Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
| |
Collapse
|
10
|
Bu J, Guo R, Xu XZ, Luo Y, Liu JF. LncRNA SNHG16 promotes epithelial-mesenchymal transition by upregulating ITGA6 through miR-488 inhibition in osteosarcoma. J Bone Oncol 2021; 27:100348. [PMID: 33598394 PMCID: PMC7868993 DOI: 10.1016/j.jbo.2021.100348] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/12/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Osteosarcoma is a primary cause of cancer-associated death in children and adolescents worldwide. Long non-coding RNAs SNHG16 (lncRNA SNHG16) and integrin subunit-a 6 (ITGA6) are recently reported to be involved in the tumorigenesis of osteosarcoma by multiple mechanisms. However, the correlation between SNHG16 and ITGA6 in osteosarcoma remains undetermined. METHODS Expression of miR-488, SNHG16 and ITGA6, as well as epithelial-mesenchymal transition (EMT) associated markers in osteosarcoma tissues and cell lines were examined by qRT-PCR or Western blotting. Effects of miR-488, SNHG16 and ITGA6 on cell migration, invasion were evaluated by wound-healing assay and transwell assay. Bioinformatics analysis and dual-luciferase reported assays were applied to assess the interaction among miR-488, SNHG16 and ITGA6. RNA immunoprecipitation (RIP) was also used to verify SNHG16 and miR-488 interaction. Finally, animal study was used to detect the effect of SNHG16 on osteosarcoma in vivo. RESULTS SNHG16 and ITGA6 were significantly increased while miR-488 was decreased in osteosarcoma. ITGA6 was screened as a target gene of miR-488, and SNHG16 was sponged by miR-488 in osteosarcoma cells. MiR-488 overexpression and SNHG16 knockdown suppressed migration, invasion and EMT of osteosarcoma cells. Moreover, rescue assays proved that the influences of SNHG16 on osteosarcoma cells migration, invasion and EMT were dependent on miR-488 and ITGA6. In addition, the promotive effects of SNHG16 on osteosarcoma tumor growth and metastasis were further supported by xenograft tumor growth assay. CONCLUSION SNHG16 promoted migration, invasion and EMT of osteosarcoma by sponging miR-488 to release ITGA6.
Collapse
Affiliation(s)
- Jie Bu
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, People's Republic of China
| | - Ru Guo
- Department of Pediatrics, Maternal and Child Health Care Hospital of Hunan Province, Changsha 410008, Hunan Province, People's Republic of China
| | - Xue-Zheng Xu
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, People's Republic of China
| | - Yi Luo
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, People's Republic of China
| | - Jian-Fan Liu
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, People's Republic of China
| |
Collapse
|
11
|
Proteasomal Regulation of Mammalian SPT16 in Controlling Transcription. Mol Cell Biol 2021; 41:MCB.00452-20. [PMID: 33526453 DOI: 10.1128/mcb.00452-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
FACT (facilitates chromatin transcription), an essential and evolutionarily conserved heterodimer from yeast to humans, controls transcription and is found to be upregulated in various cancers. However, the basis for such upregulation is not clearly understood. Our recent results deciphering a new ubiquitin-proteasome system regulation of the FACT subunit SPT16 in orchestrating transcription in yeast hint at the involvement of the proteasome in controlling FACT in humans, with a link to cancer. To test this, we carried out experiments in human embryonic kidney (HEK293) cells, which revealed that human SPT16 undergoes ubiquitylation and that its abundance is increased following inhibition of the proteolytic activity of the proteasome, thus implying proteasomal regulation of human SPT16. Furthermore, we find that the increased abundance/expression of SPT16 in HEK293 cells alters the transcription of genes, including ones associated with cancer, and that the proteasomal degradation of SPT16 is impaired in kidney cancer (Caki-2) cells to upregulate SPT16. Like human SPT16, murine SPT16 in C2C12 cells also undergoes ubiquitylation and proteasomal degradation to regulate transcription. Collectively, our results reveal a proteasomal regulation of mammalian SPT16, with physiological relevance in controlling transcription, and implicate such proteasomal control in the upregulation of SPT16 in cancer.
Collapse
|
12
|
Choi HM, Lee SH, Lee MS, Park D, Choi SS. Investigation of the putative role of antisense transcripts as regulators of sense transcripts by correlation analysis of sense-antisense pairs in colorectal cancers. FASEB J 2021; 35:e21482. [PMID: 33710708 DOI: 10.1096/fj.202002297rrr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 12/13/2022]
Abstract
Antisense transcription occurs widely more expected than when it was first identified in bacteria in the 1980s. However, the functional relevance of antisense transcripts in transcription remains controversial. Here, we investigated the putative role of antisense transcripts in regulating their corresponding sense transcripts by analyzing changes in correlative relationships between sense-antisense pairs under tumor and normal conditions. A total of 3469 sense-antisense gene pairs (SAGPs) downloaded from BioMart mapped to a list of sense and antisense genes in RNA-seq data derived from 80 paired colorectal cancer (CRC) samples were analyzed. As a result, cancer-related genes were significantly enriched in the significantly correlated SAGPs (SCPs). Differentially expressed genes estimated between normal and tumor conditions were also significantly more enriched in SCPs than in non-SCPs. Interestingly, using differential correlation analysis, we found that tumor samples had a significantly larger density of genes with higher correlation coefficients than normal samples, as verified by various cancer transcriptomes from The Cancer Genome Atlas (TCGA). Moreover, we found that the magnitude of the correlation between SAGPs could distinguish poor prognostic CRCs from good prognostic CRCs, showing that correlation coefficients between the SAGPs of CRCs with a poor prognosis were significantly stronger than CRCs with a good prognosis. Consistent with this finding, the Cox proportion hazards model showed that the survival rates were significantly different between patients with high and low expression of genes in the SCPs. All these results strongly support the idea that antisense transcripts are important regulators of their corresponding sense transcripts.
Collapse
Affiliation(s)
- Hye-Mi Choi
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, Korea
| | - Sang-Hyeop Lee
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, Korea
| | - Min-Seok Lee
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, Korea
| | | | - Sun Shim Choi
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, Korea
| |
Collapse
|
13
|
Geisinger A, Rodríguez-Casuriaga R, Benavente R. Transcriptomics of Meiosis in the Male Mouse. Front Cell Dev Biol 2021; 9:626020. [PMID: 33748111 PMCID: PMC7973102 DOI: 10.3389/fcell.2021.626020] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
Molecular studies of meiosis in mammals have been long relegated due to some intrinsic obstacles, namely the impossibility to reproduce the process in vitro, and the difficulty to obtain highly pure isolated cells of the different meiotic stages. In the recent years, some technical advances, from the improvement of flow cytometry sorting protocols to single-cell RNAseq, are enabling to profile the transcriptome and its fluctuations along the meiotic process. In this mini-review we will outline the diverse methodological approaches that have been employed, and some of the main findings that have started to arise from these studies. As for practical reasons most studies have been carried out in males, and mostly using mouse as a model, our focus will be on murine male meiosis, although also including specific comments about humans. Particularly, we will center on the controversy about gene expression during early meiotic prophase; the widespread existing gap between transcription and translation in meiotic cells; the expression patterns and potential roles of meiotic long non-coding RNAs; and the visualization of meiotic sex chromosome inactivation from the RNAseq perspective.
Collapse
Affiliation(s)
- Adriana Geisinger
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay.,Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Rosana Rodríguez-Casuriaga
- Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Ricardo Benavente
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| |
Collapse
|
14
|
Schwartz JL, Jones KL, Yeo GW. Repeat RNA expansion disorders of the nervous system: post-transcriptional mechanisms and therapeutic strategies. Crit Rev Biochem Mol Biol 2020; 56:31-53. [PMID: 33172304 PMCID: PMC8192115 DOI: 10.1080/10409238.2020.1841726] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dozens of incurable neurological disorders result from expansion of short repeat sequences in both coding and non-coding regions of the transcriptome. Short repeat expansions underlie microsatellite repeat expansion (MRE) disorders including myotonic dystrophy (DM1, CUG50–3,500 in DMPK; DM2, CCTG75–11,000 in ZNF9), fragile X tremor ataxia syndrome (FXTAS, CGG50–200 in FMR1), spinal bulbar muscular atrophy (SBMA, CAG40–55 in AR), Huntington’s disease (HD, CAG36–121 in HTT), C9ORF72-amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD and C9-ALS/FTD, GGGGCC in C9ORF72), and many others, like ataxias. Recent research has highlighted several mechanisms that may contribute to pathology in this heterogeneous class of neurological MRE disorders – bidirectional transcription, intranuclear RNA foci, and repeat associated non-AUG (RAN) translation – which are the subject of this review. Additionally, many MRE disorders share similar underlying molecular pathologies that have been recently targeted in experimental and preclinical contexts. We discuss the therapeutic potential of versatile therapeutic strategies that may selectively target disrupted RNA-based processes and may be readily adaptable for the treatment of multiple MRE disorders. Collectively, the strategies under consideration for treatment of multiple MRE disorders include reducing levels of toxic RNA, preventing RNA foci formation, and eliminating the downstream cellular toxicity associated with peptide repeats produced by RAN translation. While treatments are still lacking for the majority of MRE disorders, several promising therapeutic strategies have emerged and will be evaluated within this review.
Collapse
Affiliation(s)
- Joshua L Schwartz
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Krysten Leigh Jones
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
15
|
Grabski DF, Broseus L, Kumari B, Rekosh D, Hammarskjold ML, Ritchie W. Intron retention and its impact on gene expression and protein diversity: A review and a practical guide. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1631. [PMID: 33073477 DOI: 10.1002/wrna.1631] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/16/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Abstract
Intron retention (IR) occurs when a complete and unspliced intron remains in mature mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions, including several that impact human health and disease. Although experimental technologies used to study other forms of mRNA splicing can also be used to investigate IR, a specialized downstream computational analysis is optimal for IR discovery and analysis. Here we provide a review of IR and its biological implications, as well as a practical guide for how to detect and analyze it. Several methods, including long read third generation direct RNA sequencing, are described. We have developed an R package, FakIR, to facilitate the execution of the bioinformatic tasks recommended in this review and a tutorial on how to fit them to users aims. Additionally, we provide guidelines and experimental protocols to validate IR discovery and to evaluate the potential impact of IR on gene expression and protein output. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Splicing Regulation/Alternative Splicing RNA Methods > RNA Analyses in vitro and In Silico.
Collapse
Affiliation(s)
- David F Grabski
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA
| | - Lucile Broseus
- IGH, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Bandana Kumari
- IGH, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - William Ritchie
- IGH, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| |
Collapse
|
16
|
Complex Analysis of Retroposed Genes' Contribution to Human Genome, Proteome and Transcriptome. Genes (Basel) 2020; 11:genes11050542. [PMID: 32408516 PMCID: PMC7290577 DOI: 10.3390/genes11050542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023] Open
Abstract
Gene duplication is a major driver of organismal evolution. One of the main mechanisms of gene duplications is retroposition, a process in which mRNA is first transcribed into DNA and then reintegrated into the genome. Most gene retrocopies are depleted of the regulatory regions. Nevertheless, examples of functional retrogenes are rapidly increasing. These functions come from the gain of new spatio-temporal expression patterns, imposed by the content of the genomic sequence surrounding inserted cDNA and/or by selectively advantageous mutations, which may lead to the switch from protein coding to regulatory RNA. As recent studies have shown, these genes may lead to new protein domain formation through fusion with other genes, new regulatory RNAs or other regulatory elements. We utilized existing data from high-throughput technologies to create a complex description of retrogenes functionality. Our analysis led to the identification of human retroposed genes that substantially contributed to transcriptome and proteome. These retrocopies demonstrated the potential to encode proteins or short peptides, act as cis- and trans- Natural Antisense Transcripts (NATs), regulate their progenitors’ expression by competing for the same microRNAs, and provide a sequence to lncRNA and novel exons to existing protein-coding genes. Our study also revealed that retrocopies, similarly to retrotransposons, may act as recombination hot spots. To our best knowledge this is the first complex analysis of these functions of retrocopies.
Collapse
|
17
|
Trovero MF, Rodríguez-Casuriaga R, Romeo C, Santiñaque FF, François M, Folle GA, Benavente R, Sotelo-Silveira JR, Geisinger A. Revealing stage-specific expression patterns of long noncoding RNAs along mouse spermatogenesis. RNA Biol 2020; 17:350-365. [PMID: 31869276 PMCID: PMC6999611 DOI: 10.1080/15476286.2019.1700332] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/26/2022] Open
Abstract
The discovery of a large number of long noncoding RNAs (lncRNAs), and the finding that they may play key roles in different biological processes, have started to provide a new perspective in the understanding of gene regulation. It has been shown that the testes express the highest amount of lncRNAs among different vertebrate tissues. However, although some studies have addressed the characterization of lncRNAs along spermatogenesis, an exhaustive analysis of the differential expression of lncRNAs at its different stages is still lacking. Here, we present the results for lncRNA transcriptome profiling along mouse spermatogenesis, employing highly pure flow sorted spermatogenic stage-specific cell populations, strand-specific RNAseq, and a combination of up-to-date bioinformatic pipelines for analysis. We found that the vast majority of testicular lncRNA genes are expressed at post-meiotic stages (i.e. spermiogenesis), which are characterized by extensive post-transcriptional regulation. LncRNAs at different spermatogenic stages shared common traits in terms of transcript length, exon number, and biotypes. Most lncRNAs were lincRNAs, followed by a high representation of antisense (AS) lncRNAs. Co-expression analyses showed a high correlation along the different spermatogenic stage transitions between the expression patterns of AS lncRNAs and their overlapping protein-coding genes, raising possible clues about lncRNA-related regulatory mechanisms. Interestingly, we observed the co-localization of an AS lncRNA and its host sense mRNA in the chromatoid body, a round spermatids-specific organelle that has been proposed as a reservoir of RNA-related regulatory machinery. An additional, intriguing observation is the almost complete lack of detectable expression for Y-linked testicular lncRNAs, despite that a high number of lncRNA genes are annotated for this chromosome.
Collapse
Affiliation(s)
- María F. Trovero
- Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Rosana Rodríguez-Casuriaga
- Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Carlos Romeo
- Department of Genomics, IIBCE, Montevideo, Uruguay
| | | | - Mateo François
- Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Gustavo A. Folle
- Flow Cytometry and Cell Sorting Core, IIBCE, Montevideo, Uruguay
- Department of Genetics, IIBCE, Montevideo, Uruguay
| | - Ricardo Benavente
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - José R. Sotelo-Silveira
- Department of Genomics, IIBCE, Montevideo, Uruguay
- Department of Cell and Molecular Biology, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - Adriana Geisinger
- Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| |
Collapse
|
18
|
Wang J, Li Z, Wang X, Ding Y, Li N. The tumor suppressive effect of long non-coding RNA FRMD6-AS2 in uteri corpus endometrial carcinoma. Life Sci 2020; 243:117254. [PMID: 31917993 DOI: 10.1016/j.lfs.2020.117254] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/23/2019] [Accepted: 12/31/2019] [Indexed: 02/06/2023]
Abstract
Uterine corpus endometrial cancer (UCEC) is one of the most common gynecological malignancies with increasing incidence and high morbidity and mortality. The currently acknowledged molecular mechanism of UCEC is still not adequate. Here, we reported that the expression of a novel long non-coding RNA (lncRNA) FRMD6-AS2 was reduced in UCEC compared to noncancerous endometrium tissues using the data from The Cancer Genome Atlas (TCGA) Project database. The gene ontology (GO) analysis on differential expressed targeted genes of FRMD6-AS2 in UCEC suggested that FRMD6-AS2 might impact with the function of actin-mediated cell movement and contraction. By over-expressing FRMD6-AS2 in UCEC cell lines, we observed that FRMD6-AS2 played a suppressive role in tumor growth, migration and invasion via activation of Hippo signaling pathway including FRMD6. Moreover, we also demonstrated that FRMD6-AS2 could interact with the 30 kb upstream beyond FRMD6 and facilitate the chromatin looping towards the promoter region of FRMD6 to enhance the expression of FRMD6. We concluded that lncRNA FRMD6-AS2 repressed UCEC, at least in part, by increasing FRMD6.
Collapse
Affiliation(s)
- Jing Wang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong 264001, People's Republic of China
| | - Zenghui Li
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong 264001, People's Republic of China
| | - Xiuli Wang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong 264001, People's Republic of China
| | - Yan Ding
- Department of Spine, Yantaishan Hospital, Shandong 264001, People's Republic of China
| | - Ning Li
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Shandong 264001, People's Republic of China.
| |
Collapse
|
19
|
Chang HW, Nizovtseva EV, Razin SV, Formosa T, Gurova KV, Studitsky VM. Histone Chaperone FACT and Curaxins: Effects on Genome Structure and Function. ACTA ACUST UNITED AC 2019; 5. [PMID: 31853507 DOI: 10.20517/2394-4722.2019.31] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The histone chaperone FACT plays important roles in essentially every chromatin-associated process and is an important indirect target of the curaxin class of anti-cancer drugs. Curaxins are aromatiс compounds that intercalate into DNA and can trap FACT in bulk chromatin, thus interfering with its distribution and its functions in cancer cells. Recent studies have provided mechanistic insight into how FACT and curaxins cooperate to promote unfolding of nucleosomes and chromatin fibers, resulting in genome-wide disruption of contact chromatin domain boundaries, perturbation of higher order chromatin organization, and global disregulation of gene expression. Here, we discuss the implications of these insights for cancer biology.
Collapse
Affiliation(s)
- Han-Wen Chang
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Sergey V Razin
- Institute of Gene Biology RAS, 34/5 Vavilov Str., 119334 Moscow, Russia.,Biology Faculty, Lomonosov Moscow State University, 1 Leninskie Gory, 119992 Moscow, Russia
| | - Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
| | - Katerina V Gurova
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Elm and Carlton St, Buffalo, NY14263, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Biology Faculty, Lomonosov Moscow State University, 1 Leninskie Gory, 119992 Moscow, Russia
| |
Collapse
|