1
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Farzaneh M, Anbiyaee O, Azizidoost S, Nasrolahi A, Ghaedrahmati F, Kempisty B, Mozdziak P, Khoshnam SE, Najafi S. The Mechanisms of Long Non-coding RNA-XIST in Ischemic Stroke: Insights into Functional Roles and Therapeutic Potential. Mol Neurobiol 2024; 61:2745-2753. [PMID: 37932544 DOI: 10.1007/s12035-023-03740-x] [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: 07/01/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
Ischemic stroke, which occurs due to the occlusion of cerebral arteries, is a common type of stroke. Recent research has highlighted the important role of long non-coding RNAs (lncRNAs) in the development of cerebrovascular diseases, specifically ischemic stroke. Understanding the functional roles of lncRNAs in ischemic stroke is crucial, given their potential contribution to the disease pathology. One noteworthy lncRNA is X-inactive specific transcript (XIST), which exhibits downregulation during the early stages of ischemic stroke and subsequent upregulation in later stages. XIST exert its influence on the development of ischemic stroke through interactions with multiple miRNAs and transcription factors. These interactions play a significant role in the pathogenesis of the condition. In this review, we have provided a comprehensive summary of the functional roles of XIST in ischemic stroke. By investigating the involvement of XIST in the disease process, we aim to enhance our understanding of the mechanisms underlying ischemic stroke and potentially identify novel therapeutic targets.
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Affiliation(s)
- Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Omid Anbiyaee
- Cardiovascular Research Center, Namazi Hospital, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ava Nasrolahi
- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bartosz Kempisty
- Department of Human Morphology and Embryology, Division of Anatomy, Wroclaw Medical University, Wrocław, Poland
- Institute of Veterinary Medicine, Department of Veterinary Surgery, Nicolaus Copernicus University, Torun, Poland
- North Carolina State University College of Agriculture and Life Sciences, Raleigh, NC, 27695, USA
| | - Paul Mozdziak
- North Carolina State University College of Agriculture and Life Sciences, Raleigh, NC, 27695, USA
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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2
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Werner A, Kanhere A, Wahlestedt C, Mattick JS. Natural antisense transcripts as versatile regulators of gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00723-z. [PMID: 38632496 DOI: 10.1038/s41576-024-00723-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as a major class of gene products that have central roles in cell and developmental biology. Natural antisense transcripts (NATs) are an important subset of lncRNAs that are expressed from the opposite strand of protein-coding and non-coding genes and are a genome-wide phenomenon in both eukaryotes and prokaryotes. In eukaryotes, a myriad of NATs participate in regulatory pathways that affect expression of their cognate sense genes. Recent developments in the study of NATs and lncRNAs and large-scale sequencing and bioinformatics projects suggest that whether NATs regulate expression, splicing, stability or translation of the sense transcript is influenced by the pattern and degrees of overlap between the sense-antisense pair. Moreover, epigenetic gene regulatory mechanisms prevail in somatic cells whereas mechanisms dependent on the formation of double-stranded RNA intermediates are prevalent in germ cells. The modulating effects of NATs on sense transcript expression make NATs rational targets for therapeutic interventions.
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Affiliation(s)
| | | | | | - John S Mattick
- University of New South Wales, Sydney, New South Wales, Australia
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3
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Dror I, Chitiashvili T, Tan SYX, Cano CT, Sahakyan A, Markaki Y, Chronis C, Collier AJ, Deng W, Liang G, Sun Y, Afasizheva A, Miller J, Xiao W, Black DL, Ding F, Plath K. XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells. Cell 2024; 187:110-129.e31. [PMID: 38181737 PMCID: PMC10783549 DOI: 10.1016/j.cell.2023.11.033] [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: 12/21/2020] [Revised: 04/01/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024]
Abstract
X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.
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Affiliation(s)
- Iris Dror
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tsotne Chitiashvili
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shawn Y X Tan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Clara T Cano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Sahakyan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yolanda Markaki
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Amanda J Collier
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Weixian Deng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guohao Liang
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA
| | - Yu Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Afasizheva
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jarrett Miller
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fangyuan Ding
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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4
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Magar ND, Shah P, Barbadikar KM, Bosamia TC, Madhav MS, Mangrauthia SK, Pandey MK, Sharma S, Shanker AK, Neeraja CN, Sundaram RM. Long non-coding RNA-mediated epigenetic response for abiotic stress tolerance in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108165. [PMID: 38064899 DOI: 10.1016/j.plaphy.2023.108165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024]
Abstract
Plants perceive environmental fluctuations as stress and confront several stresses throughout their life cycle individually or in combination. Plants have evolved their sensing and signaling mechanisms to perceive and respond to a variety of stresses. Epigenetic regulation plays a critical role in the regulation of genes, spatiotemporal expression of genes under stress conditions and imparts a stress memory to encounter future stress responses. It is quintessential to integrate our understanding of genetics and epigenetics to maintain plant fitness, achieve desired genetic gains with no trade-offs, and durable long-term stress tolerance. The long non-coding RNA >200 nts having no coding potential (or very low) play several roles in epigenetic memory, contributing to the regulation of gene expression and the maintenance of cellular identity which include chromatin remodeling, imprinting (dosage compensation), stable silencing, facilitating nuclear organization, regulation of enhancer-promoter interactions, response to environmental signals and epigenetic switching. The lncRNAs are involved in a myriad of stress responses by activation or repression of target genes and hence are potential candidates for deploying in climate-resilient breeding programs. This review puts forward the significant roles of long non-coding RNA as an epigenetic response during abiotic stresses in plants and the prospects of deploying lncRNAs for designing climate-resilient plants.
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Affiliation(s)
- Nakul D Magar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India; Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Kalyani M Barbadikar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India.
| | - Tejas C Bosamia
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute, Gujarat, 364002, India
| | - M Sheshu Madhav
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Arun K Shanker
- Plant Physiology, ICAR-Central Research Institute for Dryland Agriculture, Hyderabad, 500059, India
| | - C N Neeraja
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - R M Sundaram
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
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5
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Zhang C, Zhang Y, Wang Q, Fang Z, Xu X, Zhao M, Xu T. Long non-coding RNAs in intracerebral hemorrhage. Front Mol Neurosci 2023; 16:1119275. [PMID: 37377769 PMCID: PMC10292654 DOI: 10.3389/fnmol.2023.1119275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
Intracerebral hemorrhage (ICH), a subtype of stroke, can lead to long-term disability and is one of the leading causes of death. Unfortunately, the effectiveness of pharmacological therapy for ICH is still uncertain. Long non-coding RNA (lncRNA) was defined as an RNA molecule that consists of more than 200 nt without translational activity. As a vital class of diverse molecules, lncRNAs are involved in developmental and pathological processes and have been attractive for decades. LncRNAs have also become potential targets for therapies, as they were massively identified and profiled. In particular, emerging evidence has revealed the critical role of lncRNAs in ICH while attempts were made to treat ICH via regulating lncRNAs. But the latest evidence remains to be summarized. Thus, in this review, we will summarize the recent advances in lncRNA in ICH, highlighting the regulatory role of lncRNAs and their potential as therapeutic targets.
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Affiliation(s)
- Chenyu Zhang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
- West China School of Pharmacy, Sichuan University, Chengdu, China
| | - Ying Zhang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - Qi Wang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - Zhenwei Fang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - Xinyi Xu
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
- West China School of Pharmacy, Sichuan University, Chengdu, China
| | - Mengnan Zhao
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - Ting Xu
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
- West China School of Pharmacy, Sichuan University, Chengdu, China
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6
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Ramamoorthi Elangovan V, Saadat N, Ghnenis A, Padmanabhan V, Vyas AK. Developmental programming: adverse sexually dimorphic transcriptional programming of gestational testosterone excess in cardiac left ventricle of fetal sheep. Sci Rep 2023; 13:2682. [PMID: 36792653 PMCID: PMC9932081 DOI: 10.1038/s41598-023-29212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Adverse in-utero insults during fetal life alters offspring's developmental trajectory, including that of the cardiovascular system. Gestational hyperandrogenism is once such adverse in-utero insult. Gestational testosterone (T)-treatment, an environment of gestational hyperandrogenism, manifests as hypertension and pathological left ventricular (LV) remodeling in adult ovine offspring. Furthermore, sexual dimorphism is noted in cardiomyocyte number and morphology in fetal life and at birth. This study investigated transcriptional changes and potential biomarkers of prenatal T excess-induced adverse cardiac programming. Genome-wide coding and non-coding (nc) RNA expression were compared between prenatal T-treated (T propionate 100 mg intramuscular twice weekly from days 30 to 90 of gestation; Term: 147 days) and control ovine LV at day 90 fetus in both sexes. Prenatal T induced differential expression of mRNAs in the LV of female (2 down, 5 up) and male (3 down, 1 up) (FDR < 0.05, absolute log2 fold change > 0.5); pathways analysis demonstrated 205 pathways unique to the female, 382 unique to the male and 23 common pathways. In the male, analysis of ncRNA showed differential regulation of 15 lncRNAs (14 down, 1 up) and 27 snoRNAs (26 down and 1 up). These findings suggest sexual dimorphic modulation of cardiac coding and ncRNA with gestational T excess.
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Affiliation(s)
| | - Nadia Saadat
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Adel Ghnenis
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | | | - Arpita K Vyas
- College of Medicine, California Northstate University, Elk Grove, CA, USA.
- Department of Pediatrics, Division of Pediatric Endocrinology, School of Medicine, Washington University, St Louis, MO, USA.
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7
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Mangiavacchi A, Morelli G, Orlando V. Behind the scenes: How RNA orchestrates the epigenetic regulation of gene expression. Front Cell Dev Biol 2023; 11:1123975. [PMID: 36760365 PMCID: PMC9905133 DOI: 10.3389/fcell.2023.1123975] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Non-coding DNA accounts for approximately 98.5% of the human genome. Once labeled as "junk DNA", this portion of the genome has undergone a progressive re-evaluation and it is now clear that some of its transcriptional products, belonging to the non-coding RNAs (ncRNAs), are key players in cell regulatory networks. A growing body of evidence demonstrates the crucial impact of regulatory ncRNAs on mammalian gene expression. Here, we focus on the defined relationship between chromatin-interacting RNAs, particularly long non-coding RNA (lncRNA), enhancer RNA (eRNA), non-coding natural antisense transcript (ncNAT), and circular RNA (circRNA) and epigenome, a common ground where both protein and RNA species converge to regulate cellular functions. Through several examples, this review provides an overview of the variety of targets, interactors, and mechanisms involved in the RNA-mediated modulation of loci-specific epigenetic states, a fundamental evolutive strategy to orchestrate mammalian gene expression in a timely and reversible manner. We will discuss how RNA-mediated epigenetic regulation impacts development and tissue homeostasis and how its alteration contributes to the onset and progression of many different human diseases, particularly cancer.
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8
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Iron: Not Just a Passive Bystander in AITD. Nutrients 2022; 14:nu14214682. [PMID: 36364944 PMCID: PMC9658435 DOI: 10.3390/nu14214682] [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: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Autoimmune thyroid disease (AITD) is the most prevalent autoimmune disease all over the world and the most frequent cause of hypothyroidism in areas of iodine sufficiency. The pathogenesis of AITD is multifactorial and depends on complex interactions between genetic and environmental factors, with epigenetics being the crucial link. Iron deficiency (ID) can reduce the activities of thyroid peroxidase and 5′-deiodinase, inhibit binding of triiodothyronine to its nuclear receptor, and cause slower utilization of T3 from the serum pool. Moreover, ID can disturb the functioning of the immune system, increasing the risk of autoimmune disorders. ID can be responsible for residual symptoms that may persist in patients with AITD, even if their thyrometabolic status has been controlled. The human lifestyle in the 21st century is inevitably associated with exposure to chemical compounds, pathogens, and stress, which implies an increased risk of autoimmune disorders and thyroid dysfunction. To summarize, in our paper we discuss how iron deficiency can impair the functions of the immune system, cause epigenetic changes in human DNA, and potentiate tissue damage by chemicals acting as thyroid disruptors.
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9
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Liu H, Wang D, Kan S, Hao M, Chang L, Lu P, Liu Y, Jin Y, Liu W. The role of lncRNAs and XIST in oral cancer. Front Cell Dev Biol 2022; 10:826650. [PMID: 36035993 PMCID: PMC9400023 DOI: 10.3389/fcell.2022.826650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/05/2022] [Indexed: 11/22/2022] Open
Abstract
Long non-coding RNA (lncRNA) plays a significant role in the pathogenesis of many human malignant tumors, including oral cancer. LncRNA can act as a gene regulator in a variety of cancers. It regulates the growth of malignant cells via many cellular signal pathways such as the PI3K (phosphoinositide 3-kinase)/AKT (α-serine/threonine-protein kinase) pathway. In this review, we have analyzed the role of lncRNAs, such as lncRNA X inactive specific transcript (XIST), in oral cancer, including its effects on the proliferation, apoptosis, invasion, migration, and resistance to chemotherapy of oral cancer. We have also focused on the role of lncRNA XIST as the core of X chromosome inactivation. Here, we provide a brief overview of the role of many kinds of lncRNAs, including XIST, which provides a theoretical basis for the study of the role of XIST in oral cancer. Our review may provide a new direction for the study of the occurrence, development, and prognosis of oral cancer and provide a new target for its treatment.
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Affiliation(s)
- Huimin Liu
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Shaoning Kan
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Ming Hao
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Lu Chang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
| | - Pengxu Lu
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Yangyang Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Weiwei Liu
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Hospital of Stomatology, Jilin University, Changchun, China
- *Correspondence: Weiwei Liu,
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Cao L, Luo Y, Guo X, Liu S, Li S, Li J, Zhang Z, Zhao Y, Zhang Q, Gao F, Ji X, Gao X, Li Y, You F. SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs. PLoS Pathog 2022; 18:e1010599. [PMID: 35658050 PMCID: PMC9200321 DOI: 10.1371/journal.ppat.1010599] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/15/2022] [Accepted: 05/17/2022] [Indexed: 12/19/2022] Open
Abstract
Regulation of chromatin structure and accessibility determines the transcription activities of genes, which endows the host with function-specific patterns of gene expression. Upon viral infection, the innate immune responses provide the first line of defense, allowing rapid production of variegated antiviral cytokines. Knowledge on how chromatin accessibility is regulated during host defense against viral infection remains limited. Our previous work found that the nuclear matrix protein SAFA surveilled viral RNA and regulated antiviral immune genes expression. However, how SAFA regulates the specific induction of antiviral immune genes remains unknown. Here, through integration of RNA-seq, ATAC-seq and ChIP-seq assays, we found that the depletion of SAFA specifically decreased the chromatin accessibility, activation and expression of virus induced genes. And mutation assays suggested that the RNA-binding ability of SAFA was essential for its function in regulating antiviral chromatin accessibility. RIP-seq results showed that SAFA exclusively bound with antiviral related RNAs following viral infection. Further, we combined the CRISPR-Cas13d mediated RNA knockdown system with ATAC-qPCR, and demonstrated that the binding between SAFA and according antiviral RNAs specifically mediated the openness of the corresponding chromatin and following robust transcription of antiviral genes. Moreover, knockdown of these associated RNAs dampened the accessibility of related genes in an extranuclear signaling pathway dependent manner. Interestingly, VSV infection cleaved SAFA protein at the C-terminus which deprived its RNA binding ability for immune evasion. Thus, our results demonstrated that SAFA and the interacting RNA products collaborated and remodeled chromatin accessibility to facilitate antiviral innate immune responses. Regulation of chromatin opening and gene expression underlies a key point during host defense against viral infection, which endows the host with timely and effective antiviral gene expression patterns. We previously reported that the nuclear matrix protein SAFA surveils viral RNA and regulates antiviral immune genes expression. However, how SAFA regulates the expression and what determines the specific induction of antiviral immune genes remains unclear. Here, we used a combination of high-throughput sequencing technologies and found that SAFA and the interacting RNA products collaborated and specifically remodeled chromatin accessibility to facilitate antiviral immune genes expression. We also found that VSV infection cleaved SAFA protein at the C-terminus and deprived its RNA binding ability for immune evasion. Our study provides new insights into the mechanism by which chromatin remodeling facilitates the induction of antiviral immune genes.
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Affiliation(s)
- Lili Cao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Yujie Luo
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Xuefei Guo
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Shengde Liu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Siji Li
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Junhong Li
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zeming Zhang
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Yingchi Zhao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Qiao Zhang
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Feng Gao
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of life science, Shandong University, Qingdao, China
| | - Yunfei Li
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- * E-mail: (YL); (FY)
| | - Fuping You
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- * E-mail: (YL); (FY)
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11
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Fu Y, Wang Y, Huang Q, Zhao C, Li X, Kan Y, Li D. Long Noncoding RNA lncR17454 Regulates Metamorphosis of Silkworm Through let-7 miRNA Cluster. JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:12. [PMID: 35640247 PMCID: PMC9155153 DOI: 10.1093/jisesa/ieac028] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Indexed: 06/15/2023]
Abstract
A number of long noncoding RNAs (lncRNAs) have been identified in silkworm, but little is known about their functions. Recent study showed that the let-7 miRNA cluster (contains let-7, miR-2795, and miR-100) was transcribed from the last exon of lncRNA lncR17454 in silkworm. To investigate the functional role of lncR17454, dsRNAs of lncR17454 were injected into the hemolymph of 1-d-old third-instar larvae of Bombyx mori, repression of lncR17454 led to molting arrestment during the larval-larval and larval-pupal transition of silkworm, which was consistent to the result as let-7 knockdown in other studies. The expression level of mature let-7, miR-100, and miR-2795 decreased 40%, 36%, and 40%, respectively, while the mRNA level of two predicted target genes of let-7, the Broad Complex isoform 2 (BR-C-Z2) and the BTB-Zinc finger transcription repression factor gene Abrupt (Ab), increased significantly after lncR17454 knockdown. In contrast, when adding the 20-Hydroxyecdysone (20E) to silkworm BmN4 cell lines, the expression level of lncR17454 and let-7 cluster all increased significantly, but the expression of Abrupt, the predicted target gene of let-7, was repressed. Dual-luciferase reporter assays confirmed Abrupt was the real target of let-7. Here we found that the lncRNA lncR17454 can play regulator roles in the metamorphosis of silkworm through let-7 miRNA cluster and the ecdysone signaling pathway, which will provide new clues for lepidopteran pest control.
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Affiliation(s)
| | | | - Qunxia Huang
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, China
| | - Chenyue Zhao
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, China
| | - Xinmei Li
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, China
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12
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From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo. Nat Rev Genet 2022; 23:229-243. [PMID: 34837040 DOI: 10.1038/s41576-021-00427-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide sequencing has led to the discovery of thousands of long non-coding RNA (lncRNA) loci in the human genome, but evidence of functional significance has remained controversial for many lncRNAs. Genetically engineered model organisms are considered the gold standard for linking genotype to phenotype. Recent advances in CRISPR-Cas genome editing have led to a rapid increase in the use of mouse models to more readily survey lncRNAs for functional significance. Here, we review strategies to investigate the physiological relevance of lncRNA loci by highlighting studies that have used genetic mouse models to reveal key in vivo roles for lncRNAs, from fertility to brain development. We illustrate how an investigative approach, starting with whole-gene deletion followed by transcription termination and/or transgene rescue strategies, can provide definitive evidence for the in vivo function of mammalian lncRNAs.
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13
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Ghaemi S, Fekrirad Z, Zamani N, Rahmani R, Arefian E. Non-coding RNAs Enhance the Apoptosis Efficacy of Therapeutic Agents Used for the Treatment of Glioblastoma Multiform. J Drug Target 2022; 30:589-602. [DOI: 10.1080/1061186x.2022.2047191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Shokoofeh Ghaemi
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Zahra Fekrirad
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Nina Zamani
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Rana Rahmani
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
- Pediatric Cell Therapy Research Center, Tehran University of Medical Sciences, Tehran, Iran
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14
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Focus on the Mechanisms and Functions of Pyroptosis, Inflammasomes, and Inflammatory Caspases in Infectious Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2501279. [PMID: 35132346 PMCID: PMC8817853 DOI: 10.1155/2022/2501279] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/28/2021] [Indexed: 12/17/2022]
Abstract
Eukaryotic cells can initiate several distinct self-destruction mechanisms to display essential roles for the homeostasis maintenance, development, and survival of an organism. Pyroptosis, a key response mode in innate immunity, also referred to as caspase-1-dependent proinflammatory programmed necrotic cell death activated by human caspase-1/4/5, or mouse caspase-1/11, plays indispensable roles in response to cytoplasmic insults and immune defense against infectious diseases. These inflammatory caspases are employed by the host to eliminate pathogen infections such as bacteria, viruses, protozoans, and fungi. Gasdermin D requires to be cleaved and activated by these inflammatory caspases to trigger the pyroptosis process. Physiological rupture of cells results in the release of proinflammatory cytokines, the alarmins IL-1β and IL-18, symbolizing the inflammatory potential of pyroptosis. Moreover, long noncoding RNAs play direct or indirect roles in the upstream of the pyroptosis trigger pathway. Here, we review in detail recently acquired insights into the central roles of inflammatory caspases, inflammasomes, and pyroptosis, as well as the crosstalk between pyroptosis and long noncoding RNAs in mediating infection immunity and pathogen clearance.
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15
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Kolpa HJ, Creamer KM, Hall LL, Lawrence JB. SAF-A mutants disrupt chromatin structure through dominant negative effects on RNAs associated with chromatin. Mamm Genome 2021; 33:366-381. [PMID: 34859278 PMCID: PMC9114059 DOI: 10.1007/s00335-021-09935-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022]
Abstract
Here we provide a brief review of relevant background before presenting results of our investigation into the interplay between scaffold attachment factor A (SAF-A), chromatin-associated RNAs, and DNA condensation. SAF-A, also termed heterogenous nuclear protein U (hnRNP U), is a ubiquitous nuclear scaffold protein that was implicated in XIST RNA localization to the inactive X-chromosome (Xi) but also reported to maintain open DNA packaging in euchromatin. Here we use several means to perturb SAF-A and examine potential impacts on the broad association of RNAs on euchromatin, and on chromatin compaction. SAF-A has an N-terminal DNA binding domain and C-terminal RNA binding domain, and a prominent model has been that the protein provides a single-molecule bridge between XIST RNA and chromatin. Here analysis of the impact of SAF-A on broad RNA-chromatin interactions indicate greater biological complexity. We focus on SAF-A's role with repeat-rich C0T-1 hnRNA (repeat-rich heterogeneous nuclear RNA), shown recently to comprise mostly intronic sequences of pre-mRNAs and diverse long non-coding RNAs (lncRNAs). Our results show that SAF-A mutants cause dramatic changes to cytological chromatin condensation through dominant negative effects on C0T-1 RNA's association with euchromatin, and likely other nuclear scaffold factors. In contrast, depletion of SAF-A by RNA interference (RNAi) had no discernible impact on C0T-1 RNA, nor did it cause similarly marked chromatin changes as did three different SAF-A mutations. Overall results support the concept that repeat-rich, chromatin-associated RNAs interact with multiple RNA binding proteins (RBPs) in a complex dynamic meshwork that is integral to larger-scale chromatin architecture and collectively influences cytological-scale DNA condensation.
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Affiliation(s)
- Heather J Kolpa
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.,Ashfield MedComms, Lyndhurst, NJ, 07071, USA
| | - Kevin M Creamer
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.,Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Lisa L Hall
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA. .,Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.
| | - Jeanne B Lawrence
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA. .,Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.
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16
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Maier MC, McInerney MRA, Graves JAM, Charchar FJ. Noncoding Genes on Sex Chromosomes and Their Function in Sex Determination, Dosage Compensation, Male Traits, and Diseases. Sex Dev 2021; 15:432-440. [PMID: 34794153 DOI: 10.1159/000519622] [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: 07/05/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022] Open
Abstract
The mammalian Y chromosome has evolved in many species into a specialized chromosome that contributes to sex development among other male phenotypes. This function is well studied in terms of protein-coding genes. Less is known about the noncoding genome on the Y chromosome and its contribution to both sex development and other traits. Once considered junk genetic material, noncoding RNAs are now known to contribute to the regulation of gene expression and to play an important role in refining cellular functions. The prime examples are noncoding genes on the X chromosome, which mitigate the differential dosage of genes on sex chromosomes. Here, we discuss the evolution of noncoding RNAs on the Y chromosome and the emerging evidence of how micro, long, and circular noncoding RNAs transcribed from the Y chromosome contribute to sex differentiation. We briefly touch on emerging evidence that these noncoding RNAs also contribute to some other important clinical phenotypes in humans.
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Affiliation(s)
- Michelle C Maier
- Health Innovation & Transformation Centre, Federation University, Mt Helen, Victoria, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia
| | - Molly-Rose A McInerney
- Health Innovation & Transformation Centre, Federation University, Mt Helen, Victoria, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia
| | | | - Fadi J Charchar
- Health Innovation & Transformation Centre, Federation University, Mt Helen, Victoria, Australia.,Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
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17
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Hay M, Kumar V, Ricaño-Ponce I. The role of the X chromosome in infectious diseases. Brief Funct Genomics 2021; 21:143-158. [PMID: 34651167 DOI: 10.1093/bfgp/elab039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023] Open
Abstract
Many infectious diseases in humans present with a sex bias. This bias arises from a combination of environmental factors, hormones and genetics. In this study, we review the contribution of the X chromosome to the genetic factor associated with infectious diseases. First, we give an overview of the X-linked genes that have been described in the context of infectious diseases and group them in four main pathways that seem to be dysregulated in infectious diseases: nuclear factor kappa-B, interleukin 2 and interferon γ cascade, toll-like receptors and programmed death ligand 1. Then, we review the infectious disease associations in existing genome-wide association studies (GWAS) from the GWAS Catalog and the Pan-UK Biobank, describing the main associations and their possible implications for the disease. Finally, we highlight the importance of including the X chromosome in GWAS analysis and the importance of sex-specific analysis.
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18
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Parnigoni A, Caon I, Moretto P, Viola M, Karousou E, Passi A, Vigetti D. The role of the multifaceted long non-coding RNAs: A nuclear-cytosolic interplay to regulate hyaluronan metabolism. Matrix Biol Plus 2021; 11:100060. [PMID: 34435179 PMCID: PMC8377009 DOI: 10.1016/j.mbplus.2021.100060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/03/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
In the extracellular matrix (ECM), the glycosaminoglycan (GAG) hyaluronan (HA) has different physiological roles favouring hydration, elasticity and cell survival. Three different isoforms of HA synthases (HAS1, 2, and 3) are responsible for the production of HA. In several pathologies the upregulation of HAS enzymes leads to an abnormal HA accumulation causing cell dedifferentiation, proliferation and migration thus favouring cancer progression, fibrosis and vascular wall thickening. An intriguing new player in HAS2 gene expression regulation and HA production is the long non-coding RNA (lncRNA) hyaluronan synthase 2 antisense 1 (HAS2-AS1). A significant part of mammalian genomes corresponds to genes that transcribe lncRNAs; they can regulate gene expression through several mechanisms, being involved not only in maintaining the normal homeostasis of cells and tissues, but also in the onset and progression of different diseases, as demonstrated by the increasing number of studies published through the last decades. HAS2-AS1 is no exception: it can be localized both in the nucleus and in the cytosol, regulating cancer cells as well as vascular smooth muscle cells behaviour. Hyaluronan is a component of the extracellular matrix and is synthetised by three isoenzymes named HAS1, 2, and 3. In several pathologies an upregulation of HAS2 leads to an abnormal accumulation of HA. The long non-coding RNA is a new specific epigenetic regulator of HAS2. In the nucleus HAS2-AS1 modulates chromatin structure around HAS2 promoter increasing transcription. In the cytosol, HAS2-AS1 can interact with several miRNAs altering the expression of several genes as well as can stabilise HAS2 mRNA forming RNA: RNA duplex.
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Key Words
- 4-MU, 4-methylubelliferone
- 4-MUG, 4-methylumbelliferyl glucuronide
- Atherosclerosis
- Cancer
- ECM, extracellular matrix
- EMT, epithelial to mesenchymal transition
- Epigenetics
- Extracellular matrix
- GAG, glycosaminoglycans
- Glycosaminoglycans
- HA, hyaluronan
- HAS2
- HAS2, hyaluronan synthase 2
- HAS2-AS1
- HAS2–AS1, hyaluronan synthase 2 natural antisense 1
- HIFs, hypoxia-inducible factors
- NF-κB, nuclear factor κ–light-chain enhancer of activated B cell
- PG, proteoglycan
- PTM, post-translational modification
- Proteoglycans
- RBP, RNA-binding protein
- SIRT1, sirtuin 1
- SMCs, smooth muscle cells
- TNF-α, tumour necrosis factor alpha
- UDP-GlcNAc, UDP-N-acetylglucosamine
- UDP-GlcUA, UDP-glucuronic acid
- ceRNA, competitive endogenous RNA
- lncRNA, long non-coding RNA
- miRNA, micro-RNA
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Affiliation(s)
- Arianna Parnigoni
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Ilaria Caon
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Paola Moretto
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Manuela Viola
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Evgenia Karousou
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Alberto Passi
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
| | - Davide Vigetti
- Department of Medicine and Surgery, University of Insubria, via J.H. Dunant 5, 21100 Varese, Italy
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19
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Morrison O, Thakur J. Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin. Int J Mol Sci 2021; 22:6922. [PMID: 34203193 PMCID: PMC8268097 DOI: 10.3390/ijms22136922] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 01/19/2023] Open
Abstract
Chromatin consists of a complex of DNA and histone proteins as its core components and plays an important role in both packaging DNA and regulating DNA metabolic pathways such as DNA replication, transcription, recombination, and chromosome segregation. Proper functioning of chromatin further involves a network of interactions among molecular complexes that modify chromatin structure and organization to affect the accessibility of DNA to transcription factors leading to the activation or repression of the transcription of target DNA loci. Based on its structure and compaction state, chromatin is categorized into euchromatin, heterochromatin, and centromeric chromatin. In this review, we discuss distinct chromatin factors and molecular complexes that constitute euchromatin-open chromatin structure associated with active transcription; heterochromatin-less accessible chromatin associated with silencing; centromeric chromatin-the site of spindle binding in chromosome segregation.
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Affiliation(s)
| | - Jitendra Thakur
- Department of Biology, Emory University, 1510 Clifton Rd #2006, Atlanta, GA 30322, USA;
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20
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Wang W, Min L, Qiu X, Wu X, Liu C, Ma J, Zhang D, Zhu L. Biological Function of Long Non-coding RNA (LncRNA) Xist. Front Cell Dev Biol 2021; 9:645647. [PMID: 34178980 PMCID: PMC8222981 DOI: 10.3389/fcell.2021.645647] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate gene expression in a variety of ways at epigenetic, chromatin remodeling, transcriptional, and translational levels. Accumulating evidence suggests that lncRNA X-inactive specific transcript (lncRNA Xist) serves as an important regulator of cell growth and development. Despites its original roles in X-chromosome dosage compensation, lncRNA Xist also participates in the development of tumor and other human diseases by functioning as a competing endogenous RNA (ceRNA). In this review, we comprehensively summarized recent progress in understanding the cellular functions of lncRNA Xist in mammalian cells and discussed current knowledge regarding the ceRNA network of lncRNA Xist in various diseases. Long non-coding RNAs (lncRNAs) are transcripts that are more than 200 nt in length and without an apparent protein-coding capacity (Furlan and Rougeulle, 2016; Maduro et al., 2016). These RNAs are believed to be transcribed by the approximately 98-99% non-coding regions of the human genome (Derrien et al., 2012; Fu, 2014; Montalbano et al., 2017; Slack and Chinnaiyan, 2019), as well as a large variety of genomic regions, such as exonic, tronic, and intergenic regions. Hence, lncRNAs are also divided into eight categories: Intergenic lncRNAs, Intronic lncRNAs, Enhancer lncRNAs, Promoter lncRNAs, Natural antisense/sense lncRNAs, Small nucleolar RNA-ended lncRNAs (sno-lncRNAs), Bidirectional lncRNAs, and non-poly(A) lncRNAs (Ma et al., 2013; Devaux et al., 2015; St Laurent et al., 2015; Chen, 2016; Quinn and Chang, 2016; Richard and Eichhorn, 2018; Connerty et al., 2020). A range of evidence has suggested that lncRNAs function as key regulators in crucial cellular functions, including proliferation, differentiation, apoptosis, migration, and invasion, by regulating the expression level of target genes via epigenomic, transcriptional, or post-transcriptional approaches (Cao et al., 2018). Moreover, lncRNAs detected in body fluids were also believed to serve as potential biomarkers for the diagnosis, prognosis, and monitoring of disease progression, and act as novel and potential drug targets for therapeutic exploitation in human disease (Jiang W. et al., 2018; Zhou et al., 2019a). Long non-coding RNA X-inactive specific transcript (lncRNA Xist) are a set of 15,000-20,000 nt sequences localized in the X chromosome inactivation center (XIC) of chromosome Xq13.2 (Brown et al., 1992; Debrand et al., 1998; Kay, 1998; Lee et al., 2013; da Rocha and Heard, 2017; Yang Z. et al., 2018; Brockdorff, 2019). Previous studies have indicated that lncRNA Xist regulate X chromosome inactivation (XCI), resulting in the inheritable silencing of one of the X-chromosomes during female cell development. Also, it serves a vital regulatory function in the whole spectrum of human disease (notably cancer) and can be used as a novel diagnostic and prognostic biomarker and as a potential therapeutic target for human disease in the clinic (Liu et al., 2018b; Deng et al., 2019; Dinescu et al., 2019; Mutzel and Schulz, 2020; Patrat et al., 2020; Wang et al., 2020a). In particular, lncRNA Xist have been demonstrated to be involved in the development of multiple types of tumors including brain tumor, Leukemia, lung cancer, breast cancer, and liver cancer, with the prominent examples outlined in Table 1. It was also believed that lncRNA Xist (Chaligne and Heard, 2014; Yang Z. et al., 2018) contributed to other diseases, such as pulmonary fibrosis, inflammation, neuropathic pain, cardiomyocyte hypertrophy, and osteoarthritis chondrocytes, and more specific details can be found in Table 2. This review summarizes the current knowledge on the regulatory mechanisms of lncRNA Xist on both chromosome dosage compensation and pathogenesis (especially cancer) processes, with a focus on the regulatory network of lncRNA Xist in human disease.
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Affiliation(s)
| | | | | | | | | | | | - Dongyi Zhang
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China
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21
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Epimutations and mutations, nurturing phenotypic diversity. Genetica 2021; 150:171-181. [PMID: 34114171 DOI: 10.1007/s10709-021-00124-8] [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: 11/18/2020] [Accepted: 05/26/2021] [Indexed: 12/22/2022]
Abstract
Epimutations and mutations are two dissimilar mechanisms that have contributed to the phenotypic diversities in organisms. Though dissimilar, many previous studies have revealed that the consequences of epimutations and mutations are not mutually exclusive. DNA rich in epigenetic modifications can be prone to mutations and vice versa. In order to get a better insight into the molecular evolution in organisms, it is important to consider the information of both genetic and epigenetic changes in their genomes. Understanding the similarities and differences between the consequences of epimutations and mutations is required for a better interpretation of phenotypic diversities in organisms. Factors contributing to epigenetic changes such as paramutations and mutation hotspots and, the correlation of the interdependence of mutations and epigenetic changes in DNA are important aspects that need to be considered for molecular evolutionary studies. Thus, this review explains what epimutations are, their causes, how they are similar/different from mutations, and the influence of epigenetic changes and mutations on each other, further emphasizing how molecular evolution involving both mutations and epimutations can lead to speciation. Considering this approach will aid in reorganizing taxonomic classifications, importantly, solving disparities in species identification.
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22
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Marangio P, Law KYT, Sanguinetti G, Granneman S. diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data. Genome Biol 2021; 22:165. [PMID: 34044851 PMCID: PMC8157727 DOI: 10.1186/s13059-021-02379-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 05/10/2021] [Indexed: 11/21/2022] Open
Abstract
Advancing RNA structural probing techniques with next-generation sequencing has generated demands for complementary computational tools to robustly extract RNA structural information amidst sampling noise and variability. We present diffBUM-HMM, a noise-aware model that enables accurate detection of RNA flexibility and conformational changes from high-throughput RNA structure-probing data. diffBUM-HMM is widely compatible, accounting for sampling variation and sequence coverage biases, and displays higher sensitivity than existing methods while robust against false positives. Our analyses of datasets generated with a variety of RNA probing chemistries demonstrate the value of diffBUM-HMM for quantitatively detecting RNA structural changes and RNA-binding protein binding sites.
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Affiliation(s)
- Paolo Marangio
- School of Informatics, The University of Edinburgh, Edinburgh, UK
- SISSA Data Science Excellence Department Initiative, Trieste, Italy
| | - Ka Ying Toby Law
- Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh, UK
| | - Guido Sanguinetti
- Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh, UK.
- School of Informatics, The University of Edinburgh, Edinburgh, UK.
- SISSA Data Science Excellence Department Initiative, Trieste, Italy.
| | - Sander Granneman
- Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh, UK.
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23
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Moisan MP. Sexual Dimorphism in Glucocorticoid Stress Response. Int J Mol Sci 2021; 22:ijms22063139. [PMID: 33808655 PMCID: PMC8003420 DOI: 10.3390/ijms22063139] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/16/2021] [Indexed: 12/18/2022] Open
Abstract
Chronic stress is encountered in our everyday life and is thought to contribute to a number of diseases. Many of these stress-related disorders display a sex bias. Because glucocorticoid hormones are the main biological mediator of chronic stress, researchers have been interested in understanding the sexual dimorphism in glucocorticoid stress response to better explain the sex bias in stress-related diseases. Although not yet demonstrated for glucocorticoid regulation, sex chromosomes do influence sex-specific biology as soon as conception. Then a transient rise in testosterone start to shape the male brain during the prenatal period differently to the female brain. These organizational effects are completed just before puberty. The cerebral regions implicated in glucocorticoid regulation at rest and after stress are thereby impacted in a sex-specific manner. After puberty, the high levels of all gonadal hormones will interact with glucocorticoid hormones in specific crosstalk through their respective nuclear receptors. In addition, stress occurring early in life, in particular during the prenatal period and in adolescence will prime in the long-term glucocorticoid stress response through epigenetic mechanisms, again in a sex-specific manner. Altogether, various molecular mechanisms explain sex-specific glucocorticoid stress responses that do not exclude important gender effects in humans.
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24
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Zhao Y, Chen Y, Jin M, Wang J. The crosstalk between m 6A RNA methylation and other epigenetic regulators: a novel perspective in epigenetic remodeling. Am J Cancer Res 2021; 11:4549-4566. [PMID: 33754077 PMCID: PMC7977459 DOI: 10.7150/thno.54967] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/07/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic regulation involves a range of sophisticated processes which contribute to heritable alterations in gene expression without altering DNA sequence. Regulatory events predominantly include DNA methylation, chromatin remodeling, histone modifications, non-coding RNAs (ncRNAs), and RNA modification. As the most prevalent RNA modification in eukaryotic cells, N6-methyladenosine (m6A) RNA methylation actively participates in the modulation of RNA metabolism. Notably, accumulating evidence has revealed complicated interrelations occurring between m6A and other well-known epigenetic modifications. Their crosstalk conspicuously triggers epigenetic remodeling, further yielding profound impacts on a variety of physiological and pathological processes, especially tumorigenesis. Herein, we provide an up-to-date review of this emerging hot area of biological research, summarizing the interplay between m6A RNA methylation and other epigenetic regulators, and highlighting their underlying functions in epigenetic reprogramming.
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25
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Ohhata T, Yamazawa K, Miura-Kamio A, Takahashi S, Sakai S, Tamura Y, Uchida C, Kitagawa K, Niida H, Hiratani I, Kobayashi H, Kimura H, Wutz A, Kitagawa M. Dynamics of transcription-mediated conversion from euchromatin to facultative heterochromatin at the Xist promoter by Tsix. Cell Rep 2021; 34:108912. [PMID: 33789104 DOI: 10.1016/j.celrep.2021.108912] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/08/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
The fine-scale dynamics from euchromatin (EC) to facultative heterochromatin (fHC) has remained largely unclear. Here, we focus on Xist and its silencing initiator Tsix as a paradigm of transcription-mediated conversion from EC to fHC. In mouse epiblast stem cells, induction of Tsix recapitulates the conversion at the Xist promoter. Investigating the dynamics reveals that the conversion proceeds in a stepwise manner. Initially, a transient opened chromatin structure is observed. In the second step, gene silencing is initiated and dependent on Tsix, which is reversible and accompanied by simultaneous changes in multiple histone modifications. At the last step, maintenance of silencing becomes independent of Tsix and irreversible, which correlates with occupation of the -1 position of the transcription start site by a nucleosome and initiation of DNA methylation introduction. This study highlights the hierarchy of multiple chromatin events upon stepwise gene silencing establishment.
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Affiliation(s)
- Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan.
| | - Kazuki Yamazawa
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo 152-8902, Japan
| | - Asuka Miura-Kamio
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Saori Takahashi
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Satoshi Sakai
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Yuka Tamura
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Chiharu Uchida
- Advanced Research Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Kyoko Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Masatoshi Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan.
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26
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Bacon ER, Brinton RD. Epigenetics of the developing and aging brain: Mechanisms that regulate onset and outcomes of brain reorganization. Neurosci Biobehav Rev 2021; 125:503-516. [PMID: 33657435 DOI: 10.1016/j.neubiorev.2021.02.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/11/2022]
Abstract
Brain development is a life-long process that encompasses several critical periods of transition, during which significant cognitive changes occur. Embryonic development, puberty, and reproductive senescence are all periods of transition that are hypersensitive to environmental factors. Rather than isolated episodes, each transition builds upon the last and is influenced by consequential changes that occur in the transition before it. Epigenetic marks, such as DNA methylation and histone modifications, provide mechanisms by which early events can influence development, cognition, and health outcomes. For example, parental environment influences imprinting patterns in gamete cells, which ultimately impacts gene expression in the embryo which may result in hypersensitivity to poor maternal nutrition during pregnancy, raising the risks for cognitive impairment later in life. This review explores how epigenetics induce and regulate critical periods, and also discusses how early environmental interactions prime a system towards a particular health outcome and influence susceptibility to disease or cognitive impairment throughout life.
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Affiliation(s)
- Eliza R Bacon
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; The Center for Precision Medicine, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Roberta Diaz Brinton
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; Center for Innovation in Brain Science, School of Medicine, University of Arizona, Tucson, AZ, 85721, USA.
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27
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Bonner C, Sproule A, Rowland O, Overy D, Subramaniam R. DNA Methylation Is Responsive to the Environment and Regulates the Expression of Biosynthetic Gene Clusters, Metabolite Production, and Virulence in Fusarium graminearum. FRONTIERS IN FUNGAL BIOLOGY 2021; 1:614633. [PMID: 37743878 PMCID: PMC10512235 DOI: 10.3389/ffunb.2020.614633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 09/26/2023]
Abstract
Histone modifications play a significant role in the regulation of biosynthetic gene clusters (BGCs) in the phytopathogen Fusarium graminearum, by contrast, epigenetic regulation by DNA methyltransferases (DNMTs) is less documented. In this study, we characterized two DNMTs (FgDIM-2 and FgRID) in F. graminearum, with homologies to "Deficient in methylation" (DIM-2) and "Repeat-induced point (RIP) deficient" (RID) from Neurospora. The loss of DNMTs resulted in not only a decrease in average methylation density in the nutrient-poor, compared to nutrient-rich conditions, but also differences in the genes expressed between the WT and the DNMT mutant strains, implicating the external environment as an important trigger in altering DNA methylation patterns. Consequently, we observed significant changes in the regulation of multiple BGCs and alterations in the pathogenicity of the fungus.
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Affiliation(s)
- Christopher Bonner
- Department of Biology, Carleton University, Ottawa, ON, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Amanda Sproule
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Owen Rowland
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - David Overy
- Department of Biology, Carleton University, Ottawa, ON, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Rajagopal Subramaniam
- Department of Biology, Carleton University, Ottawa, ON, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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28
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Constanty F, Shkumatava A. lncRNAs in development and differentiation: from sequence motifs to functional characterization. Development 2021; 148:148/1/dev182741. [PMID: 33441380 DOI: 10.1242/dev.182741] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The number of long noncoding RNAs (lncRNAs) with characterized developmental and cellular functions continues to increase, but our understanding of the molecular mechanisms underlying lncRNA functions, and how they are dictated by RNA sequences, remains limited. Relatively short, conserved sequence motifs embedded in lncRNA transcripts are often important determinants of lncRNA localization, stability and interactions. Identifying such RNA motifs remains challenging due to the substantial length of lncRNA transcripts and the rapid evolutionary turnover of lncRNA sequences. Nevertheless, the recent discovery of specific RNA elements, together with their experimental interrogation, has enabled the first step in classifying heterogeneous lncRNAs into sub-groups with similar molecular mechanisms and functions. In this Review, we focus on lncRNAs with roles in development, cell differentiation and normal physiology in vertebrates, and we discuss the sequence elements defining their functions. We also summarize progress on the discovery of regulatory RNA sequence elements, as well as their molecular functions and interaction partners.
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Affiliation(s)
- Florian Constanty
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
| | - Alena Shkumatava
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris 75005, France
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29
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Busan S, Weeks KM. Visualization of lncRNA and mRNA Structure Models Within the Integrative Genomics Viewer. Methods Mol Biol 2021; 2254:15-25. [PMID: 33326067 PMCID: PMC7935467 DOI: 10.1007/978-1-0716-1158-6_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Every class of RNA forms base-paired structures that impact biological functions. Chemical probing of RNA structure, especially with the advent of strategies such as SHAPE-MaP, vastly expands the scale and quantitative accuracy over which RNA structure can be examined. These methods have enabled large-scale structural studies of mRNAs and lncRNAs, but the length and complexity of these RNAs makes interpretation of the data challenging. We have created modules available through the open-source Integrative Genomics Viewer (IGV) for straightforward visualization of RNA structures along with complementary experimental data. Here we present detailed and stepwise strategies for exploring and visualizing complex RNA structures in IGV. Individuals can use these instructions and supplied sample data to become adept at using IGV to visualize RNA structure models in conjunction with useful allied information.
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Affiliation(s)
- Steven Busan
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA.
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30
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Ramírez-Colmenero A, Oktaba K, Fernandez-Valverde SL. Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans. Front Genet 2020; 11:589697. [PMID: 33329735 PMCID: PMC7734150 DOI: 10.3389/fgene.2020.589697] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have important regulatory functions across eukarya. It is now clear that many of these functions are related to gene expression regulation through their capacity to recruit epigenetic modifiers and establish chromatin interactions. Several lncRNAs have been recently shown to participate in modulating chromatin within the spatial organization of the genome in the three-dimensional space of the nucleus. The identification of lncRNA candidates is challenging, as it is their functional characterization. Conservation signatures of lncRNAs are different from those of protein-coding genes, making identifying lncRNAs under selection a difficult task, and the homology between lncRNAs may not be readily apparent. Here, we review the evidence for these higher-order genome organization functions of lncRNAs in animals and the evolutionary signatures they display.
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Affiliation(s)
- América Ramírez-Colmenero
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Katarzyna Oktaba
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Selene L Fernandez-Valverde
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
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31
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Feng B, Li S, Wang Q, Tang L, Huang F, Zhang Z, Mahboobe S, Shao C. lncRNA DMRT2-AS acts as a transcriptional regulator of dmrt2 involving in sex differentiation in the Chinese tongue sole (Cynoglossus semilaevis). Comp Biochem Physiol B Biochem Mol Biol 2020; 253:110542. [PMID: 33301875 DOI: 10.1016/j.cbpb.2020.110542] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/17/2022]
Abstract
Long non-coding RNAs (lncRNAs) contribute to various biological processes, including sexual development. As a member of the DMRT family, dmrt2 plays a very important role in sex determination and differentiation. In this study, we cloned and characterized the lncRNA DMRT2-AS (referred to as dmrt2 antisense) associated with dmrt2 from the gonads of the Chinese tongue sole (Cynoglossus semilaevis). The full-length cDNA of DMRT2-AS was 537 bp. Based on a sequence alignment, DMRT2-AS overlapped with dmrt2 in reverse on exon 4 and intron 3, with a region of overlap of 221 bp on exon 4. RT-qPCR showed that DMRT2-AS was highly expressed in the testis of Chinese tongue sole. In addition, the expression of DMRT2-AS increased continuously during male gonadal development. In vitro experiments and bioinformatics predictions showed that DMRT2-AS promoted the expression of dmrt2 at the transcriptional level. These results suggest that DMRT2-AS acts as a transcriptional regulator of dmrt2 and plays an important role in the gonadal differentiation of male.
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Affiliation(s)
- Bo Feng
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Shuo Li
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ningbo University, Ningbo 315211, China
| | - Qian Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China
| | - Lili Tang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China
| | - Fei Huang
- Genosys, Inc., Shenzhen 518000, China
| | - Zhihua Zhang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Shahid Mahboobe
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China.
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32
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Qi Y, Reyes A, Johnstone SE, Aryee MJ, Bernstein BE, Zhang B. Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization. Biophys J 2020; 119:1905-1916. [PMID: 33086041 DOI: 10.1016/j.bpj.2020.09.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/24/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Chromosomes are positioned nonrandomly inside the nucleus to coordinate with their transcriptional activity. The molecular mechanisms that dictate the global genome organization and the nuclear localization of individual chromosomes are not fully understood. We introduce a polymer model to study the organization of the diploid human genome. It is data-driven because all parameters can be derived from Hi-C data; it is also a mechanistic model because the energy function is explicitly written out based on a few biologically motivated hypotheses. These two features distinguish the model from existing approaches and make it useful both for reconstructing genome structures and for exploring the principles of genome organization. We carried out extensive validations to show that simulated genome structures reproduce a wide variety of experimental measurements, including chromosome radial positions and spatial distances between homologous pairs. Detailed mechanistic investigations support the importance of both specific interchromosomal interactions and centromere clustering for chromosome positioning. We anticipate the polymer model, when combined with Hi-C experiments, to be a powerful tool for investigating large-scale rearrangements in genome structure upon cell differentiation and tumor progression.
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Affiliation(s)
- Yifeng Qi
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Alejandro Reyes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Data Sciences, Dana Farber Cancer Institute, Boston, Massachusetts; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Sarah E Johnstone
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Bin Zhang
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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33
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DNA Methylation in Pulmonary Fibrosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:51-62. [PMID: 32949389 DOI: 10.1007/978-981-15-4494-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
DNA methylations, including global methylation pattern and specific gene methylation, are associated with pathogenesis and progress of pulmonary fibrosis. This chapter illustrates alteration of DNA methylation in pulmonary fibrosis as a predictive or prognostic factor. Treatment with the DNA methylation inhibitors will be an emerging anti-fibrosis therapy, although we are still in the pre-clinical stage of using epigenetic markers as potential targets for biomarkers and therapeutic interventions.
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34
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The influence of DNA methylation on monoallelic expression. Essays Biochem 2020; 63:663-676. [PMID: 31782494 PMCID: PMC6923323 DOI: 10.1042/ebc20190034] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 01/02/2023]
Abstract
Monoallelic gene expression occurs in diploid cells when only one of the two alleles of a gene is active. There are three main classes of genes that display monoallelic expression in mammalian genomes: (1) imprinted genes that are monoallelically expressed in a parent-of-origin dependent manner; (2) X-linked genes that undergo random X-chromosome inactivation in female cells; (3) random monoallelically expressed single and clustered genes located on autosomes. The heritability of monoallelic expression patterns during cell divisions implies that epigenetic mechanisms are involved in the cellular memory of these expression states. Among these, methylation of CpG sites on DNA is one of the best described modification to explain somatic inheritance. Here, we discuss the relevance of DNA methylation for the establishment and maintenance of monoallelic expression patterns among these three groups of genes, and how this is intrinsically linked to development and cellular states.
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35
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Wei C, Zhao L, Liang H, Zhen Y, Han L. Recent advances in unraveling the molecular mechanisms and functions of HOXA11‑AS in human cancers and other diseases (Review). Oncol Rep 2020; 43:1737-1754. [PMID: 32236611 PMCID: PMC7160552 DOI: 10.3892/or.2020.7552] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
A large number of previously published research articles have demonstrated that the expression levels of long noncoding RNAs (lncRNAs) are generally dysregulated, either through overexpression or underexpression, in cancer and other types of disease. As a recently discovered lncRNA, HOXA11 antisense RNA (HOXA11‑AS) is able to serve as an oncogenic or tumor‑suppressor gene and serves a vital role in the processes of proliferation, invasion, and migration of cancer cells. HOXA11‑AS appears to be a major factor contributing to epigenetic modification, and exerts transcriptional, post‑transcriptional, translational and post‑translational regulatory effects on genes through a variety of mechanisms; for example, by competing endogenous RNA (ceRNA) and a molecular scaffold mechanism. A number of reports have demonstrated that HOXA11‑AS functions as a protein scaffold for polycomb repressive complex 2 (PRC2), lysine‑specific histone demethylase 1 (LSD1) and DNA methyltransferase 1 (DNMT1) to perform epigenetic modifications on chromosomes in the nucleus. Furthermore, HOXA11‑AS is also located in the cytoplasm and can act as a ceRNA, which sponges miRNAs. In addition, HOXA11‑AS may be useful as a biomarker for the diagnosis and prognosis of cancer. In the present review article, the clinical value, phenotype and mechanism of HOXA11‑AS in a variety of tumors types are briefly summarized, as well as its clinical value in certain additional diseases. The perspective of the authors is that HOXA11‑AS may represent an effective tumor marker and therapeutic target for cancer diagnosis and therapy.
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Affiliation(s)
- Cheng Wei
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Liangjuan Zhao
- Tianjin Customs District China, Heping, Tianjin 300041, P.R. China
| | - Hao Liang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Yingwei Zhen
- Department of Neurosurgery, The First Affliated Hospital of Zhengzhou University, Zhengzhou, Henan 453002, P.R. China
| | - Lei Han
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
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36
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Winge SB, Soraggi S, Schierup MH, Rajpert-De Meyts E, Almstrup K. Integration and reanalysis of transcriptomics and methylomics data derived from blood and testis tissue of men with 47,XXY Klinefelter syndrome indicates the primary involvement of Sertoli cells in the testicular pathogenesis. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:239-255. [PMID: 32449318 DOI: 10.1002/ajmg.c.31793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/03/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022]
Abstract
Klinefelter syndrome (KS; 47,XXY) is the most common sex chromosomal anomaly and causes a multitude of symptoms. Often the most noticeable symptom is infertility caused by azoospermia with testicular histology showing hyalinization of tubules, germ cells loss, and Leydig cell hyperplasia. The germ cell loss begins early in life leading to partial hyalinization of the testis at puberty, but the mechanistic drivers behind this remain poorly understood. In this systematic review, we summarize the current knowledge on developmental changes in the cellularity of KS gonads supplemented by a comparative analysis of the fetal and adult gonadal transcriptome, and blood transcriptome and methylome of men with KS. We identified a high fraction of upregulated genes that escape X-chromosome inactivation, thus supporting previous hypotheses that these are the main drivers of the testicular phenotype in KS. Enrichment analysis showed overrepresentation of genes from the X- and Y-chromosome and testicular transcription factors. Furthermore, by re-evaluation of recent single cell RNA-sequencing data originating from adult KS testis, we found novel evidence that the Sertoli cell is the most affected cell type. Our results are consistent with disturbed cross-talk between somatic and germ cells in the KS testis, and with X-escapee genes acting as mediators.
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Affiliation(s)
- Sofia B Winge
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Samuele Soraggi
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | | | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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37
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Brooks W. An Epigenetics-Based Hypothesis of Autoantigen Development in Systemic Lupus Erythematosus. EPIGENOMES 2020; 4:epigenomes4020006. [PMID: 34968240 PMCID: PMC8594704 DOI: 10.3390/epigenomes4020006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/20/2020] [Indexed: 11/16/2022] Open
Abstract
Currently, we have a limited understanding of mechanisms leading to systemic lupus erythematosus, but we know that genetics, environmental factors, and epigenetics contribute to the disease. One common aspect of the various environmental triggers is that they can cause cellular stress. When extraordinary stress occurs, such as viral activation, a cell's response can include increased nucleolar volume and activity to produce more machinery (e.g., ribosomes) to help the cell recover. However, nucleolar expansion can disrupt the epigenetic control in neighboring heterochromatin that comprises the nucleolar shell. This disruption can open underlying vulnerabilities that provoke an autoimmune reaction. Here, we review the "X chromosome-nucleolus nexus" hypothesis, which explains how nucleolar stress can disrupt epigenetically silenced chromatin, especially the neighboring inactive X chromosome (aka the nucleolar satellite). Chromatin disruption can lead to the expression of sequestered DNA, such as Alu elements and fully functional LINE-1 reverse transcriptase genes. In addition, Alu transcripts can disrupt the nucleolar structural integrity, leading to nucleolar disintegration. Such disintegration can leave nucleolar components and products in autoantigenic forms, such as abnormal conformations or incomplete macromolecular assemblies. Recent research on DNA sensing pathways can now be incorporated into the hypothesis to provide further details explaining how autoantibodies to endogenous nucleic acids arise.
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Affiliation(s)
- Wesley Brooks
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
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38
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Coker H, Wei G, Moindrot B, Mohammed S, Nesterova T, Brockdorff N. The role of the Xist 5' m6A region and RBM15 in X chromosome inactivation. Wellcome Open Res 2020; 5:31. [PMID: 32258426 PMCID: PMC7097882 DOI: 10.12688/wellcomeopenres.15711.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2020] [Indexed: 12/14/2022] Open
Abstract
Background: X chromosome inactivation in mammals is regulated by the non-coding (nc) RNA, Xist, which represses the chromosome from which it is transcribed. High levels of the N6-methyladenosine (m6A) RNA modification occur within Xist exon I, close to the 5' end of the transcript, and also further 3', in Xist exon VII. The m6A modification is catalysed by the METTL3/14 complex that is directed to specific targets, including Xist, by the RNA binding protein RBM15/15B. m6A modification of Xist RNA has been reported to be important for Xist-mediated gene silencing. Methods: We use CRISPR/Cas9 mediated mutagenesis to delete sequences around the 5' m6A region in interspecific XX mouse embryonic stem cells (mESCs). Following induction of Xist RNA expression, we assay chromosome silencing using allelic RNA-seq and Xist m6A distribution using m6A-seq. Additionally, we use Xist RNA FISH to analyse the effect of deleting the 5' m6A region on the function of the endogenous Xist promoter. We purify epitope tagged RBM15 from mESCs, and then apply MS/MS analysis to define the RBM15 interactome. Results: We show that a deletion encompassing the entire Xist 5' m6A region results in a modest reduction in Xist-mediated silencing, and that the 5' m6A region overlaps essential DNA elements required for activation of the endogenous Xist promoter. Deletion of the Xist A-repeat, to which RBM15 binds, entirely abolishes deposition of m6A in the Xist 5' m6A region without affecting the modification in exon VII. We show that in mESCs, RBM15 interacts with the m6A complex, the SETD1B histone modifying complex, and several proteins linked to RNA metabolism. Conclusions: Our findings support that RBM15 binding to the Xist A-repeat recruits the m6A complex to the 5' Xist m6A region and that this region plays a role in Xist-mediated chromosome silencing.
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Affiliation(s)
- Heather Coker
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Benoit Moindrot
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Shabaz Mohammed
- Proteomics Technology Development and Application, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tatyana Nesterova
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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Kong S, Zhou C, Bao H, Ni Z, Liu M, He B, Huang L, Sun Y, Wang H, Lu J. Epigenetic control of embryo-uterine crosstalk at peri-implantation. Cell Mol Life Sci 2019; 76:4813-4828. [PMID: 31352535 PMCID: PMC11105790 DOI: 10.1007/s00018-019-03245-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 06/28/2019] [Accepted: 07/23/2019] [Indexed: 01/05/2023]
Abstract
Embryo implantation is one of the pivotal steps during mammalian pregnancy, since the quality of embryo implantation determines the outcome of ongoing pregnancy and fetal development. A large number of factors, including transcription factors, signalling transduction components, and lipids, have been shown to be indispensable for embryo implantation. Increasing evidence also suggests the important roles of epigenetic factors in this critical event. This review focuses on recent findings about the involvement of epigenetic regulators during embryo implantation.
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Affiliation(s)
- Shuangbo Kong
- Reproductive Medical Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Chan Zhou
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Haili Bao
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Zhangli Ni
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Mengying Liu
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Bo He
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Lin Huang
- Reproductive Medical Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Yang Sun
- Reproductive Medical Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, People's Republic of China
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China
| | - Haibin Wang
- Reproductive Medical Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, People's Republic of China.
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China.
| | - Jinhua Lu
- Reproductive Medical Center, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, People's Republic of China.
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China.
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Abstract
In mammals, dosage compensation of sex chromosomal genes between females (XX) and males (XY) is achieved through X-chromosome inactivation (XCI). The X-linked X-inactive-specific transcript (Xist) long noncoding RNA is indispensable for XCI and initiates the process early during development by spreading in cis across the X chromosome from which it is transcribed. During XCI, Xist RNA triggers gene silencing, recruits a plethora of chromatin modifying factors, and drives a major structural reorganization of the X chromosome. Here, we review our knowledge of the multitude of epigenetic events orchestrated by Xist RNA to allow female mammals to survive through embryonic development by establishing and maintaining proper dosage compensation. In particular, we focus on recent studies characterizing the interaction partners of Xist RNA, and we discuss how they have affected the field by addressing long-standing controversies or by giving rise to new research perspectives that are currently being explored. This review is dedicated to the memory of Denise Barlow, pioneer of genomic imprinting and functional long noncoding RNAs (lncRNAs), whose work has revolutionized the epigenetics field and continues to inspire generations of scientists.
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Lobo J, Nunes SP, Gillis AJM, Barros-Silva D, Miranda-Gonçalves V, Berg AVD, Cantante M, Guimarães R, Henrique R, Jerónimo C, Looijenga LHJ. XIST-Promoter Demethylation as Tissue Biomarker for Testicular Germ Cell Tumors and Spermatogenesis Quality. Cancers (Basel) 2019; 11:E1385. [PMID: 31533343 PMCID: PMC6769809 DOI: 10.3390/cancers11091385] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The event of X chromosome inactivation induced by XIST, which is physiologically observed in females, is retained in testicular germ cell tumors (TGCTs), as a result of a supernumerary X chromosome constitution. X chromosome inactivation also occurs in male germline, specifically during spermatogenesis. We aimed to analyze the promoter methylation status of XIST in a series of TGCT tissues, representative cell lines, and testicular parenchyma. METHODS Two independent cohorts were included, comprising a total of 413 TGCT samples, four (T)GCT cell lines, and 86 testicular parenchyma samples. The relative amount of methylated and demethylated XIST promoter fragments was assessed by quantitative methylation-specific PCR (qMSP) and more sensitive high-resolution melting (HRM) methylation analyses. RESULTS Seminomas showed a lower amount of methylated XIST fragments as compared to non-seminomas or normal testis (p < 0.0001), allowing for a good discrimination among these groups (area under the curve 0.83 and 0.81, respectively). Seminomas showed a significantly higher content of demethylated XIST as compared to non-seminomas. The percentage of demethylated XIST fragment in cell lines reflected their chromosomal constitution (number of extra X chromosomes). A novel and strong positive correlation between the Johnsen's score and XIST demethylation was identified (r = 0.75, p < 0.0001). CONCLUSIONS The X chromosome inactivation event and demethylated XIST promoter are promising biomarkers for TGCTs and for assessing spermatogenesis quality.
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Affiliation(s)
- João Lobo
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands.
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal.
| | - Sandra P Nunes
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
| | - Ad J M Gillis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands.
| | - Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
| | - Vera Miranda-Gonçalves
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
| | - Annette van den Berg
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands.
| | - Mariana Cantante
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
| | - Rita Guimarães
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal.
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) and Porto Comprehensive Cancer Center (P.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal.
| | - Leendert H J Looijenga
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands.
- Department of Pathology, Lab. for Exp. Patho-Oncology (LEPO), Erasmus MC-University Medical Center Rotterdam, Cancer Institute, Be-432A, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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Zhang J, Li WY, Yang Y, Yan LZ, Zhang SY, He J, Wang JX. LncRNA XIST facilitates cell growth, migration and invasion via modulating H3 histone methylation of DKK1 in neuroblastoma. Cell Cycle 2019; 18:1882-1892. [PMID: 31208278 PMCID: PMC6681787 DOI: 10.1080/15384101.2019.1632134] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been confirmed to be aberrantly expressed and involved in the progression of neuroblastoma. This study aimed to explore the expression profile of lncRNA X-inactive specific transcript (XIST) and its functional involvement in neuroblastoma. In this study, the relative level of XIST in neuroblastoma tissues and cell lines was detected by qPCR, and DKK1 protein expression was determined using western blot. The effect of XIST on cell growth, invasion and migration in vitro and in tumorigenesis of neuroblastoma was assessed. The level of H3K27me3 in DKK1 promoter was analyzed with ChIP-qPCR. Interaction between XIST and EZH2 was verified by RNA immunoprecipitation (RIP) and RNA pull-down assay. XIST was significantly upregulated in neuroblastoma tissues (n = 30) and cells lines, and it was statistically associated with the age and International Neuroblastoma Staging System (INSS) staging in neuroblastoma patients. Downregulation of XIST suppressed the growth, migration and invasion of neuroblastoma cells. EZH2 inhibited DKK1 expression through inducing H3 histone methylation in its promoter. XIST increased the level of H3K27me3 in DKK1 promoter via interacting with EZH2. Downregulation of XIST increased DKK1 expression to suppress neuroblastoma cell growth, invasion, and migration, which markedly restrained the tumor progression. In conclusion, XIST downregulated DKK1 by inducing H3 histone methylation via EZH2, thereby facilitating the growth, migration and invasion of neuroblastoma cells and retarding tumor progression.
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Affiliation(s)
- Jiao Zhang
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- CONTACT Jiao Zhang
| | - Wen-Ya Li
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Yang
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Li-Zhao Yan
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Song-Yang Zhang
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jia-Xiang Wang
- Department of Pediatric Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Nesterova TB, Wei G, Coker H, Pintacuda G, Bowness JS, Zhang T, Almeida M, Bloechl B, Moindrot B, Carter EJ, Alvarez Rodrigo I, Pan Q, Bi Y, Song CX, Brockdorff N. Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation. Nat Commun 2019; 10:3129. [PMID: 31311937 PMCID: PMC6635394 DOI: 10.1038/s41467-019-11171-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 06/19/2019] [Indexed: 01/05/2023] Open
Abstract
Xist RNA, the master regulator of X chromosome inactivation, acts in cis to induce chromosome-wide silencing. Whilst recent studies have defined candidate silencing factors, their relative contribution to repressing different genes, and their relationship with one another is poorly understood. Here we describe a systematic analysis of Xist-mediated allelic silencing in mouse embryonic stem cell-based models. Using a machine learning approach we identify distance to the Xist locus and prior gene expression levels as key determinants of silencing efficiency. We go on to show that Spen, recruited through the Xist A-repeat, plays a central role, being critical for silencing of all except a subset of weakly expressed genes. Polycomb, recruited through the Xist B/C-repeat, also plays a key role, favouring silencing of genes with pre-existing H3K27me3 chromatin. LBR and the Rbm15/m6A-methyltransferase complex make only minor contributions to gene silencing. Together our results provide a comprehensive model for Xist-mediated chromosome silencing.
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Affiliation(s)
- Tatyana B Nesterova
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Heather Coker
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Greta Pintacuda
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Joseph S Bowness
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Tianyi Zhang
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mafalda Almeida
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Bianca Bloechl
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Benoit Moindrot
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- I2BC Paris-Sud University, Gif-Sur-Yvette, France
| | - Emma J Carter
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Ines Alvarez Rodrigo
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Qi Pan
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Ying Bi
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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Barros de Andrade E Sousa L, Jonkers I, Syx L, Dunkel I, Chaumeil J, Picard C, Foret B, Chen CJ, Lis JT, Heard E, Schulz EG, Marsico A. Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features. Genome Res 2019; 29:1087-1099. [PMID: 31175153 PMCID: PMC6633258 DOI: 10.1101/gr.245027.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 05/28/2019] [Indexed: 01/12/2023]
Abstract
To initiate X-Chromosome inactivation (XCI), the long noncoding RNA Xist mediates chromosome-wide gene silencing of one X Chromosome in female mammals to equalize gene dosage between the sexes. The efficiency of gene silencing is highly variable across genes, with some genes even escaping XCI in somatic cells. A gene's susceptibility to Xist-mediated silencing appears to be determined by a complex interplay of epigenetic and genomic features; however, the underlying rules remain poorly understood. We have quantified chromosome-wide gene silencing kinetics at the level of the nascent transcriptome using allele-specific Precision nuclear Run-On sequencing (PRO-seq). We have developed a Random Forest machine-learning model that can predict the measured silencing dynamics based on a large set of epigenetic and genomic features and tested its predictive power experimentally. The genomic distance to the Xist locus, followed by gene density and distance to LINE elements, are the prime determinants of the speed of gene silencing. Moreover, we find two distinct gene classes associated with different silencing pathways: a class that requires Xist-repeat A for silencing, which is known to activate the SPEN pathway, and a second class in which genes are premarked by Polycomb complexes and tend to rely on the B repeat in Xist for silencing, known to recruit Polycomb complexes during XCI. Moreover, a series of features associated with active transcriptional elongation and chromatin 3D structure are enriched at rapidly silenced genes. Our machine-learning approach can thus uncover the complex combinatorial rules underlying gene silencing during X inactivation.
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Affiliation(s)
| | - Iris Jonkers
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Laurène Syx
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 75005 Paris, France
- Institut Curie, PSL Research University, Mines Paris Tech, INSERM U900, 75005 Paris, France
| | - Ilona Dunkel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Julie Chaumeil
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 75005 Paris, France
| | - Christel Picard
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 75005 Paris, France
| | - Benjamin Foret
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 75005 Paris, France
| | - Chong-Jian Chen
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 75005 Paris, France
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Edith Heard
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, UPMC Paris-Sorbonne, 75005 Paris, France
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Annalisa Marsico
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Department of Mathematics and Informatics, Free University of Berlin, 14195 Berlin, Germany
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Piro RM, Marsico A. Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations. Methods Mol Biol 2019; 1912:301-321. [PMID: 30635899 DOI: 10.1007/978-1-4939-8982-9_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The discovery that a considerable portion of eukaryotic genomes is transcribed and gives rise to long noncoding RNAs (lncRNAs) provides an important new perspective on the transcriptome and raises questions about the centrality of these lncRNAs in gene-regulatory processes and diseases. The rapidly increasing number of mechanistically investigated lncRNAs has provided evidence for distinct functional classes, such as enhancer-like lncRNAs, which modulate gene expression via chromatin looping, and noncoding competing endogenous RNAs (ceRNAs), which act as microRNA decoys. Despite great progress in the last years, the majority of lncRNAs are functionally uncharacterized and their implication for disease biogenesis and progression is unknown. Here, we summarize recent developments in lncRNA function prediction in general and lncRNA-disease associations in particular, with emphasis on in silico methods based on network analysis and on ceRNA function prediction. We believe that such computational techniques provide a valuable aid to prioritize functional lncRNAs or disease-relevant lncRNAs for targeted, experimental follow-up studies.
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Affiliation(s)
- Rosario Michael Piro
- Institut für Informatik, Freie Universität Berlin, Berlin, Germany.,Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annalisa Marsico
- Institut für Informatik, Freie Universität Berlin, Berlin, Germany. .,Max-Planck-Institut für molekulare Genetik, Berlin, Germany.
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A novel approach to differentiate rat embryonic stem cells in vitro reveals a role for RNF12 in activation of X chromosome inactivation. Sci Rep 2019; 9:6068. [PMID: 30988473 PMCID: PMC6465393 DOI: 10.1038/s41598-019-42246-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 03/27/2019] [Indexed: 02/07/2023] Open
Abstract
X chromosome inactivation (XCI) is a mammalian specific, developmentally regulated process relying on several mechanisms including antisense transcription, non-coding RNA-mediated silencing, and recruitment of chromatin remodeling complexes. In vitro modeling of XCI, through differentiation of embryonic stem cells (ESCs), provides a powerful tool to study the dynamics of XCI, overcoming the need for embryos, and facilitating genetic modification of key regulatory players. However, to date, robust initiation of XCI in vitro has been mostly limited to mouse pluripotent stem cells. Here, we adapted existing protocols to establish a novel monolayer differentiation protocol for rat ESCs to study XCI. We show that differentiating rat ESCs properly downregulate pluripotency factor genes, and present female specific Xist RNA accumulation and silencing of X-linked genes. We also demonstrate that RNF12 seems to be an important player in regulation of initiation of XCI in rat, acting as an Xist activator. Our work provides the basis to investigate the mechanisms directing the XCI process in a model organism different from the mouse.
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47
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Mendonça ADS, Silveira MM, Rios ÁFL, Mangiavacchi PM, Caetano AR, Dode MAN, Franco MM. DNA methylation and functional characterization of the XIST gene during in vitro early embryo development in cattle. Epigenetics 2019; 14:568-588. [PMID: 30925851 DOI: 10.1080/15592294.2019.1600828] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
XIST, in association with the shorter ncRNA RepA, are essential for the initiation of X chromosome inactivation (XCI) in mice. The molecular mechanisms controlling XIST and RepA expression are well characterized in that specie. However, little is known in livestock. We aimed to characterize the DNA methylation status along the 5' portion of XIST and to characterize its transcriptional profile during early development in cattle. Three genomic regions of XIST named here as promoter, RepA and DMR1 had their DNA methylation status characterized in gametes and embryos. Expression profile of XIST was evaluated, including sense and antisense transcription. Oocytes showed higher levels of methylation than spermatozoa that was demethylated. DMR1 was hypermethylated throughout oogenesis. At the 8-16-cell embryo stage DMR1 was completed demethylated. Interestingly, RepA gain methylation during oocyte maturation and was demethylated at the blastocyst stage, later than DMR1. These results suggest that DMR1 and RepA are transient differentially methylated regions in cattle. XIST RNA was detected in matured oocytes and in single cells from the 2-cell to the morula stage, confirming the presence of maternal and embryonic transcripts. Sense and antisense transcripts were detected along the XIST in blastocyst. In silico analysis identified 63 novel transcript candidates at bovine XIST locus from both the plus and minus strands. Taking together these results improve our understanding of the molecular mechanisms involved in XCI initiation in cattle. This information may be useful for the improvement of assisted reproductive technologies in livestock considering that in vitro conditions may impair epigenetic reprogramming.
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Affiliation(s)
- Anelise Dos Santos Mendonça
- a Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology , Parque Estação Biológica , Brasília , Brazil.,b Institute of Genetics and Biochemistry , Federal University of Uberlândia , Umuarama , Brazil.,c Federal Institute of Education, Science and Technology of Piauí , Uruçuí Campus , Portal dos Cerrados , Brazil
| | - Márcia Marques Silveira
- a Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology , Parque Estação Biológica , Brasília , Brazil.,b Institute of Genetics and Biochemistry , Federal University of Uberlândia , Umuarama , Brazil
| | - Álvaro Fabrício Lopes Rios
- d Biotechnology Laboratory, Center of Biosciences and Biotechnology , North Fluminense State University , Campos dos Goytacazes , Brazil
| | - Paula Magnelli Mangiavacchi
- e Laboratory of Reproduction and Animal Genetic Improvement, Center for Agricultural Sciences and Technologies , North Fluminense State University , Campos dos Goytacazes , Brazil
| | - Alexandre Rodrigues Caetano
- f Embrapa Genetic Resources and Biotechnology , Parque Estação Biológica , Brasília , Brazil.,g School of Agriculture and Veterinary Medicine , University of Brasília, Darcy Ribeiro Campus , Brasília , Brazil
| | - Margot Alves Nunes Dode
- a Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology , Parque Estação Biológica , Brasília , Brazil.,g School of Agriculture and Veterinary Medicine , University of Brasília, Darcy Ribeiro Campus , Brasília , Brazil
| | - Maurício Machaim Franco
- a Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology , Parque Estação Biológica , Brasília , Brazil.,b Institute of Genetics and Biochemistry , Federal University of Uberlândia , Umuarama , Brazil.,h Faculty of Veterinary Medicine , Federal University of Uberlândia , Umuarama , Brazil
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48
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Zhao X, Ruan Z, Qin X, Feng Y, Yu Q, Xu J, Deng Y, Shen P, Shi D, Lu F. The Role of 5-aza-2'-Deoxycytidine on Methylation Status of Xist Gene in Different Genders of Buffalo (Bubalus bubalis) Bone Marrow Mesenchymal Stem Cells. Cell Reprogram 2019; 21:89-98. [PMID: 30785778 DOI: 10.1089/cell.2018.0040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Previous studies have demonstrated that proper concentration of 5-aza-2'-deoxycytidine (5-aza-CdR) treatment was advantageous to decrease DNA methylation level, but the relationships between 5-aza-CdR treatment and methylation status of imprinted genes are seldom detected. The aim of this study was to investigate the effect of low concentration 5-aza-CdR treatment on the methylation status of imprinted gene Xist in different genders of buffalo bone marrow mesenchymal stem cells (BMSCs). BMSCs were isolated and the cell gender was identified through polymerase chain reaction (PCR). Then different concentrations of 5-aza-CdR (0, 0.02, 0.1 μM) were applied for the treatment. The results showed cellular morphology, growth, Xist gene expression pattern, and adherent ability were not significantly affected with the treatment of 5-aza-CdR for 24 hours. Meanwhile, immunofluorescence analysis indicated that the expression of 5-methylcytosine (5-mC) was also not influenced after the treatment. However, bisulfite sequence PCR (BS-PCR) analysis revealed that the methylation level of Xist differentially methylated region (DMR) decreased significantly when the concentration of 5-aza-CdR increased to 0.1 μM in the ♀BMSCs group (p < 0.05), while there was no significant difference among the ♂BMSCs-treated groups. Our results implied that low concentrations of 5-aza-CdR treatment had little impacts on cellular morphology, growth Xist gene expression pattern, adherent ability, and global DNA methylation level of BMSCs in both genders, but the treatment could significantly decrease the methylation level of Xist DMR in ♀BMSCs. Thus, we conclude 5-aza-CdR treatment can affect the methylation status of Xist DMR, furthermore, the influence is also related to sex differences.
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Affiliation(s)
- Xin Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Ziyun Ruan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Xiling Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Yun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Qing Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Jie Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Yanfei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Penglei Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Fenghua Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
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49
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Karlik E, Ari S, Gozukirmizi N. LncRNAs: genetic and epigenetic effects in plants. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1581085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Elif Karlik
- Department of Biotechnology Institute of Graduate Studies in Science and Engineering, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
| | - Sule Ari
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
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50
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Li L, Zhuang Y, Zhao X, Li X. Long Non-coding RNA in Neuronal Development and Neurological Disorders. Front Genet 2019; 9:744. [PMID: 30728830 PMCID: PMC6351443 DOI: 10.3389/fgene.2018.00744] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/27/2018] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts which are usually more than 200 nt in length, and which do not have the protein-coding capacity. LncRNAs can be categorized based on their generation from distinct DNA elements, or derived from specific RNA processing pathways. During the past several decades, dramatic progress has been made in understanding the regulatory functions of lncRNAs in diverse biological processes, including RNA processing and editing, cell fate determination, dosage compensation, genomic imprinting and development etc. Dysregulation of lncRNAs is involved in multiple human diseases, especially neurological disorders. In this review, we summarize the recent progress made with regards to the function of lncRNAs and associated molecular mechanisms, focusing on neuronal development and neurological disorders.
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Affiliation(s)
- Ling Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yingliang Zhuang
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xingsen Zhao
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xuekun Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
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