1
|
Du Z, Hu L, Zou Z, Liu M, Li Z, Lu X, Harris C, Xiang Y, Chen F, Yu G, Xu K, Kong F, Xu Q, Huang B, Liu L, Fan Q, Wang H, Kalantry S, Xie W. Stepwise de novo establishment of inactive X chromosome architecture in early development. Nat Genet 2024:10.1038/s41588-024-01897-2. [PMID: 39256583 DOI: 10.1038/s41588-024-01897-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/07/2024] [Indexed: 09/12/2024]
Abstract
X chromosome inactivation triggers a dramatic reprogramming of transcription and chromosome architecture. However, how the chromatin organization of inactive X chromosome is established de novo in vivo remains elusive. Here, we identified an Xist-separated megadomain structure (X-megadomains) on the inactive X chromosome in mouse extraembryonic lineages and extraembryonic endoderm (XEN) cell lines, and transiently in the embryonic lineages, before Dxz4-delineated megadomain formation at later stages in a strain-specific manner. X-megadomain boundary coincides with strong enhancer activities and cohesin binding in an Xist regulatory region required for proper Xist activation in early embryos. Xist regulatory region disruption or cohesin degradation impaired X-megadomains in extraembryonic endoderm cells and caused ectopic activation of regulatory elements and genes near Xist, indicating that cohesin loading at regulatory elements promotes X-megadomains and confines local gene activities. These data reveal stepwise X chromosome folding and transcriptional regulation to achieve both essential gene activation and global silencing during the early stages of X chromosome inactivation.
Collapse
Affiliation(s)
- Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Liangjun Hu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zhuoning Zou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Meishuo Liu
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zihan Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xukun Lu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yunlong Xiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Fengling Chen
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Guang Yu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qianhua Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Bo Huang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Haifeng Wang
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
| |
Collapse
|
2
|
Das S, Zea Rojas MP, Tran EJ. Novel insights on the positive correlation between sense and antisense pairs on gene expression. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1864. [PMID: 39087253 DOI: 10.1002/wrna.1864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 08/02/2024]
Abstract
A considerable proportion of the eukaryotic genome undergoes transcription, leading to the generation of noncoding RNA molecules that lack protein-coding information and are not subjected to translation. These noncoding RNAs (ncRNAs) are well recognized to have essential roles in several biological processes. Long noncoding RNAs (lncRNAs) represent the most extensive category of ncRNAs found in the human genome. Much research has focused on investigating the roles of cis-acting lncRNAs in the regulation of specific target gene expression. In the majority of instances, the regulation of sense gene expression by its corresponding antisense pair occurs in a negative (discordant) manner, resulting in the suppression of the target genes. The notion that a negative correlation exists between sense and antisense pairings is, however, not universally valid. In fact, several recent studies have reported a positive relationship between corresponding cis antisense pairs within plants, budding yeast, and mammalian cancer cells. The positive (concordant) correlation between anti-sense and sense transcripts leads to an increase in the level of the sense transcript within the same genomic loci. In addition, mechanisms such as altering chromatin structure, the formation of R loops, and the recruitment of transcription factors can either enhance transcription or stabilize sense transcripts through their antisense pairs. The primary objective of this work is to provide a comprehensive understanding of both aspects of antisense regulation, specifically focusing on the positive correlation between sense and antisense transcripts in the context of eukaryotic gene expression, including its implications towards cancer progression. This article is categorized under: RNA Processing > 3' End Processing Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
Collapse
Affiliation(s)
- Subhadeep Das
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Purdue University Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | | | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Purdue University Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| |
Collapse
|
3
|
Maldonado R, Längst G. The chromatin - triple helix connection. Biol Chem 2023; 404:1037-1049. [PMID: 37506218 DOI: 10.1515/hsz-2023-0189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
Mammalian genomes are extensively transcribed, producing a large number of coding and non-coding transcripts. A large fraction of the nuclear RNAs is physically associated with chromatin, functioning in gene activation and silencing, shaping higher-order genome organisation, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions. Different mechanisms allow the tethering of these chromatin-associated RNAs (caRNA) to chromosomes, including RNA binding proteins, the RNA polymerases and R-loops. In this review, we focus on the sequence-specific targeting of RNA to DNA by forming triple helical structures and describe its interplay with chromatin. It turns out that nucleosome positioning at triple helix target sites and the nucleosome itself are essential factors in determining the formation and stability of triple helices. The histone H3-tail plays a critical role in triple helix stabilisation, and the role of its epigenetic modifications in this process is discussed.
Collapse
Affiliation(s)
- Rodrigo Maldonado
- Institute of Anatomy, Histology, and Pathology, Faculty of Medicine, Universidad Austral de Chile, 5090000 Valdivia, Chile
| | - Gernot Längst
- Regensburg Center for Biochemistry (RCB), University of Regensburg, D-93053 Regensburg, Germany
| |
Collapse
|
4
|
Jaiswal A, Kaushik N, Choi EH, Kaushik NK. Functional impact of non-coding RNAs in high-grade breast carcinoma: Moving from resistance to clinical applications: A comprehensive review. Biochim Biophys Acta Rev Cancer 2023; 1878:188915. [PMID: 37196783 DOI: 10.1016/j.bbcan.2023.188915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/08/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Despite the recent advances in cancer therapy, triple-negative breast cancers (TNBCs) are the most relapsing cancer sub-type. It is partly due to their propensity to develop resistance against the available therapies. An intricate network of regulatory molecules in cellular mechanisms leads to the development of resistance in tumors. Non-coding RNAs (ncRNAs) have gained widespread attention as critical regulators of cancer hallmarks. Existing research suggests that aberrant expression of ncRNAs modulates the oncogenic or tumor suppressive signaling. This can mitigate the responsiveness of efficacious anti-tumor interventions. This review presents a systematic overview of biogenesis and down streaming molecular mechanism of the subgroups of ncRNAs. Furthermore, it explains ncRNA-based strategies and challenges to target the chemo-, radio-, and immunoresistance in TNBCs from a clinical standpoint.
Collapse
Affiliation(s)
- Apurva Jaiswal
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Suwon 18323, Republic of Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| |
Collapse
|
5
|
Wang R, Shiu HT, Lee WYW. Emerging role of lncRNAs in osteoarthritis: An updated review. Front Immunol 2022; 13:982773. [PMID: 36304464 PMCID: PMC9593085 DOI: 10.3389/fimmu.2022.982773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Osteoarthritis (OA) is a prevalent joint disease, which is associated with progressive articular cartilage loss, synovial inflammation, subchondral sclerosis and meniscus injury. The molecular mechanism underlying OA pathogenesis is multifactorial. Long non-coding RNAs (lncRNAs) are non-protein coding RNAs with length more than 200 nucleotides. They have various functions such as modulating transcription and protein activity, as well as forming endogenous small interfering RNAs (siRNAs) and microRNA (miRNA) sponges. Emerging evidence suggests that lncRNAs might be involved in the pathogenesis of OA which opens up a new avenue for the development of new biomarkers and therapeutic strategies. The purpose of this review is to summarize the current clinical and basic experiments related to lncRNAs and OA with a focus on the extensively studied H19, GAS5, MALAT1, XIST and HOTAIR. The potential translational value of these lncRNAs as therapeutic targets for OA is also discussed.
Collapse
Affiliation(s)
- Rongliang Wang
- Department of Orthopaedics and Traumatology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- SH Ho Scoliosis Research Laboratory, Joint Scoliosis Research Center of the Chinese University of Hong Kong and Nanjing University, The Chinese University of Hong Kong, Hong Kong, China
| | - Hoi Ting Shiu
- Department of Orthopaedics and Traumatology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wayne Yuk Wai Lee
- Department of Orthopaedics and Traumatology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- SH Ho Scoliosis Research Laboratory, Joint Scoliosis Research Center of the Chinese University of Hong Kong and Nanjing University, The Chinese University of Hong Kong, Hong Kong, China
- *Correspondence: Wayne Yuk Wai Lee,
| |
Collapse
|
6
|
Fontaine E, Papin C, Martinez G, Le Gras S, Nahed RA, Héry P, Buchou T, Ouararhni K, Favier B, Gautier T, Sabir JSM, Gerard M, Bednar J, Arnoult C, Dimitrov S, Hamiche A. Dual role of histone variant H3.3B in spermatogenesis: positive regulation of piRNA transcription and implication in X-chromosome inactivation. Nucleic Acids Res 2022; 50:7350-7366. [PMID: 35766398 PMCID: PMC9303386 DOI: 10.1093/nar/gkac541] [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: 06/04/2021] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/21/2022] Open
Abstract
The histone variant H3.3 is encoded by two distinct genes, H3f3a and H3f3b, exhibiting identical amino-acid sequence. H3.3 is required for spermatogenesis, but the molecular mechanism of its spermatogenic function remains obscure. Here, we have studied the role of each one of H3.3A and H3.3B proteins in spermatogenesis. We have generated transgenic conditional knock-out/knock-in (cKO/KI) epitope-tagged FLAG-FLAG-HA-H3.3B (H3.3BHA) and FLAG-FLAG-HA-H3.3A (H3.3AHA) mouse lines. We show that H3.3B, but not H3.3A, is required for spermatogenesis and male fertility. Analysis of the molecular mechanism unveils that the absence of H3.3B led to alterations in the meiotic/post-meiotic transition. Genome-wide RNA-seq reveals that the depletion of H3.3B in meiotic cells is associated with increased expression of the whole sex X and Y chromosomes as well as of both RLTR10B and RLTR10B2 retrotransposons. In contrast, the absence of H3.3B resulted in down-regulation of the expression of piRNA clusters. ChIP-seq experiments uncover that RLTR10B and RLTR10B2 retrotransposons, the whole sex chromosomes and the piRNA clusters are markedly enriched of H3.3. Taken together, our data dissect the molecular mechanism of H3.3B functions during spermatogenesis and demonstrate that H3.3B, depending on its chromatin localization, is involved in either up-regulation or down-regulation of expression of defined large chromatin regions.
Collapse
Affiliation(s)
- Emeline Fontaine
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante' - Allée des Alpes, La Tronche 38700, France
| | - Christophe Papin
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/ CNRS/INSERM, 67404 Illkirch Cedex, France
| | - Guillaume Martinez
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante' - Allée des Alpes, La Tronche 38700, France
| | - Stéphanie Le Gras
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/ CNRS/INSERM, 67404 Illkirch Cedex, France
| | - Roland Abi Nahed
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante' - Allée des Alpes, La Tronche 38700, France
| | - Patrick Héry
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Thierry Buchou
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante' - Allée des Alpes, La Tronche 38700, France
| | - Khalid Ouararhni
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/ CNRS/INSERM, 67404 Illkirch Cedex, France
| | - Bertrand Favier
- Université de Grenoble Alpes, Etablissement Français du Sang, EA 7408, BP35, 38701 La Tronche, France
| | - Thierry Gautier
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante' - Allée des Alpes, La Tronche 38700, France
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Matthieu Gerard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Jan Bednar
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante' - Allée des Alpes, La Tronche 38700, France
| | - Christophe Arnoult
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante' - Allée des Alpes, La Tronche 38700, France
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Sante' - Allée des Alpes, La Tronche 38700, France.,"Roumen Tsanev" Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.,Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35330, Turkey
| | - Ali Hamiche
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/ CNRS/INSERM, 67404 Illkirch Cedex, France.,Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| |
Collapse
|
7
|
Liu N, Xu Y, Li Q, Cao Y, Yang D, Liu S, Wang X, Mi Y, Liu Y, Ding C, Liu Y, Li Y, Yuan YW, Gao G, Chen J, Qian W, Zhang X. A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth. Cell Host Microbe 2022; 30:1124-1138.e8. [DOI: 10.1016/j.chom.2022.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/07/2022] [Accepted: 06/17/2022] [Indexed: 11/03/2022]
|
8
|
Vourc’h C, Dufour S, Timcheva K, Seigneurin-Berny D, Verdel A. HSF1-Activated Non-Coding Stress Response: Satellite lncRNAs and Beyond, an Emerging Story with a Complex Scenario. Genes (Basel) 2022; 13:genes13040597. [PMID: 35456403 PMCID: PMC9032817 DOI: 10.3390/genes13040597] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 12/21/2022] Open
Abstract
In eukaryotes, the heat shock response is orchestrated by a transcription factor named Heat Shock Factor 1 (HSF1). HSF1 is mostly characterized for its role in activating the expression of a repertoire of protein-coding genes, including the heat shock protein (HSP) genes. Remarkably, a growing set of reports indicate that, upon heat shock, HSF1 also targets various non-coding regions of the genome. Focusing primarily on mammals, this review aims at reporting the identity of the non-coding genomic sites directly bound by HSF1, and at describing the molecular function of the long non-coding RNAs (lncRNAs) produced in response to HSF1 binding. The described non-coding genomic targets of HSF1 are pericentric Satellite DNA repeats, (sub)telomeric DNA repeats, Short Interspersed Nuclear Element (SINE) repeats, transcriptionally active enhancers and the NEAT1 gene. This diverse set of non-coding genomic sites, which already appears to be an integral part of the cellular response to stress, may only represent the first of many. Thus, the study of the evolutionary conserved heat stress response has the potential to emerge as a powerful cellular context to study lncRNAs, produced from repeated or unique DNA regions, with a regulatory function that is often well-documented but a mode of action that remains largely unknown.
Collapse
Affiliation(s)
- Claire Vourc’h
- Université de Grenoble Alpes (UGA), 38700 La Tronche, France
- Correspondence: (C.V.); (A.V.)
| | - Solenne Dufour
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
| | - Kalina Timcheva
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
| | - Daphné Seigneurin-Berny
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
| | - André Verdel
- Institute for Advanced Biosciences (IAB), Centre de Recherche UGA/Inserm U 1209/CNRS UMR 5309, Site Santé-Allée des Alpes, 38700 La Tronche, France; (S.D.); (K.T.); (D.S.-B.)
- Correspondence: (C.V.); (A.V.)
| |
Collapse
|
9
|
Wan Y, Gu C, Kong J, Sui J, Zuo L, Song Y, Chen J. Long noncoding RNA ADAMTS9-AS1 represses ferroptosis of endometrial stromal cells by regulating the miR-6516-5p/GPX4 axis in endometriosis. Sci Rep 2022; 12:2618. [PMID: 35173188 PMCID: PMC8850595 DOI: 10.1038/s41598-022-04963-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/22/2021] [Indexed: 12/18/2022] Open
Abstract
Endometriosis (EMs) is one of the most frequent diseases of reproductive-age women and is characterized by the growth of endometrial tissues beyond the uterus. The enhanced proliferative and migratory potential of endometrial stromal cells (ESCs) plays an important role in the progression of EMs. Mounting studies have demonstrated that long noncoding RNAs (lncRNAs) exert an important role in regulating the development and progression of EMs. Given the aberrant expression of lncRNA ADAMTS9-AS1 in ectopic endometrium (ecEM), we investigated the biological effect of ADAMTS9-AS1 on ESC proliferation and migration and explored the underlying mechanism. The current data showed that ADAMTS9-AS1 expression was significantly upregulated in ecEM compared with eutopic endometrium (euEM) in patients with EMs and in a murine model of EMs. Functionally, ADAMTS9-AS1 knockdown in ectopic ESCs (EESCs) decreased cell viability and migration, whereas ADAMTS9-AS1 overexpression in normal ESCs (NESCs) enhanced cell viability and migration. More importantly, the effect of ADAMTS9-AS1 inhibition on decreasing ESC viability was significantly blocked by ferrostatin-1 (Fer-1, a ferroptosis inhibitor), and ADAMTS9-AS1 overexpression repressed erastin (a ferroptosis activator)-induced cell death. Furthermore, the regulatory role of ADAMTS9-AS1 in ferroptosis was defined and evidenced by increased reactive oxygen species (ROS) levels and malonyl dialdehyde (MDA) content and decreased expression of glutathione peroxidase 4 (GPX4) after ADAMTS9-AS1 inhibition. Mechanistically, ADAMTS9-AS1 functioned as a competing endogenous RNA (ceRNA) by sponging miR-6516-5p to derepress the expression of GPX4, the critical repressor of ferroptosis. Taken together, these results demonstrate that upregulated ADAMTS9-AS1 accelerates ESC proliferation and migration by regulating miR-6516-5p/GPX4-dependent ferroptosis and may be a potential target for the treatment of EMs.
Collapse
Affiliation(s)
- Yiting Wan
- Department of Gynecology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, No. 274 Middle Zhijiang Road, Shanghai, 200071, China
| | - Cancan Gu
- Department of Gynecology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, No. 274 Middle Zhijiang Road, Shanghai, 200071, China
| | - Jueying Kong
- Department of Gynecology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, No. 274 Middle Zhijiang Road, Shanghai, 200071, China
| | - Jin Sui
- Department of Gynecology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, No. 274 Middle Zhijiang Road, Shanghai, 200071, China
| | - Ling Zuo
- Department of Gynecology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, No. 274 Middle Zhijiang Road, Shanghai, 200071, China
| | - Yanhua Song
- Department of Gynecology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, No. 274 Middle Zhijiang Road, Shanghai, 200071, China.
| | - Jing Chen
- Department of Gynecology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, No. 274 Middle Zhijiang Road, Shanghai, 200071, China.
| |
Collapse
|
10
|
Zhang L, Wang X. Lowly expressed LNC01136 fails to aid HIF-1α to induce BTG2 expression resulting in increased proliferation of retinal microvascular endothelial cells. Microvasc Res 2022; 141:104315. [PMID: 35007537 DOI: 10.1016/j.mvr.2022.104315] [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: 09/14/2021] [Revised: 11/30/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Retinal neovascularization (RN), a major cause of blindness occurring in multiple types of ophthalmic diseases, is closely associated with hypoxic conditions. However, the underlying pathological mechanisms of RN have not been fully elucidated. BTG2 is anti-proliferative factor. The up-stream of BTG2 gene within 3000 bp expresses a long non-coding RNA, LNC01136. METHODS we initially compared the expression of BTG2 and LNC01136 in human retinal microvascular endothelial cells (hRMECs) with other eye-associated cells, including Muller cells, ARPE19 cells and RGC-5, in response to a hypoxia mimetic agent (CoCl2). FISH and PCR tests were performed to determine the enrichment of LNC01136 in different cellular components. LNC01136 were overexpressed or knockdown to determine the effect on BTG2 expression. Finally, ChIP, RIP and Co-IP assays were performed to determine the interaction among BTG2, HIF-1α, LNC01136 and CNOT7. RESULTS After the treatment with CoCl2, expression levels of BTG2 and LNC01136 were strongly induced in Muller cells, ARPE19 cells and RGC-5, but weakly in hRMECs. LNC01136 is prominently located in cell nucleus and aids HIF-1α to enhance transcription of BTG2, which consequently inhibits cell growth. The anti-proliferative effect of BTG2 is probably associated to the interaction with CNOT7 and the regulation of multiple cell cycle-related proteins. CONCLUSIONS This study revealed that LNC01136 is a cell growth suppressor by recruiting HIF-1α to induce BTG2 expression. However the low expression of LNC01136 in hRMECs compared to other eye-associated cells promoted hRMECs' proliferation, which is probably a cause of RN under hypoxia.
Collapse
Affiliation(s)
- Lixin Zhang
- Department of Ophthalmology, Hunan Children's Hospital, Changsha 410006, PR China
| | - Xilang Wang
- Department of Ophthalmology, Hunan Children's Hospital, Changsha 410006, PR China.
| |
Collapse
|
11
|
Raposo AC, Casanova M, Gendrel AV, da Rocha ST. The tandem repeat modules of Xist lncRNA: a swiss army knife for the control of X-chromosome inactivation. Biochem Soc Trans 2021; 49:2549-2560. [PMID: 34882219 PMCID: PMC8786293 DOI: 10.1042/bst20210253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 12/16/2022]
Abstract
X-inactive-specific transcript (Xist) is a long non-coding RNA (lncRNA) essential for X-chromosome inactivation (XCI) in female placental mammals. Thirty years after its discovery, it is still puzzling how this lncRNA triggers major structural and transcriptional changes leading to the stable silencing of an entire chromosome. Recently, a series of studies in mouse cells have uncovered domains of functional specialization within Xist mapping to conserved tandem repeat regions, known as Repeats A-to-F. These functional domains interact with various RNA binding proteins (RBPs) and fold into distinct RNA structures to execute specific tasks in a synergistic and coordinated manner during the inactivation process. This modular organization of Xist is mostly conserved in humans, but recent data point towards differences regarding functional specialization of the tandem repeats between the two species. In this review, we summarize the recent progress on understanding the role of Xist repetitive blocks and their involvement in the molecular mechanisms underlying XCI. We also discuss these findings in the light of the similarities and differences between mouse and human Xist.
Collapse
Affiliation(s)
- Ana Cláudia Raposo
- Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Casanova
- Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Simão Teixeira da Rocha
- Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
12
|
Oh HJ, Aguilar R, Kesner B, Lee HG, Kriz AJ, Chu HP, Lee JT. Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops. Cell 2021; 184:6157-6173.e24. [PMID: 34856126 DOI: 10.1016/j.cell.2021.11.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 01/24/2023]
Abstract
Chromosome loops shift dynamically during development, homeostasis, and disease. CCCTC-binding factor (CTCF) is known to anchor loops and construct 3D genomes, but how anchor sites are selected is not yet understood. Here, we unveil Jpx RNA as a determinant of anchor selectivity. Jpx RNA targets thousands of genomic sites, preferentially binding promoters of active genes. Depleting Jpx RNA causes ectopic CTCF binding, massive shifts in chromosome looping, and downregulation of >700 Jpx target genes. Without Jpx, thousands of lost loops are replaced by de novo loops anchored by ectopic CTCF sites. Although Jpx controls CTCF binding on a genome-wide basis, it acts selectively at the subset of developmentally sensitive CTCF sites. Specifically, Jpx targets low-affinity CTCF motifs and displaces CTCF protein through competitive inhibition. We conclude that Jpx acts as a CTCF release factor and shapes the 3D genome by regulating anchor site usage.
Collapse
Affiliation(s)
- Hyun Jung Oh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Rodrigo Aguilar
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Barry Kesner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Hun-Goo Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Andrea J Kriz
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Hsueh-Ping Chu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
| |
Collapse
|
13
|
Liu C, Lin P, Zhao J, Xie H, Li R, Yang X, Wang N, Jia H, Jiang S, Zhang K, Yu X. Knockdown of long noncoding RNA AC245100.4 inhibits the tumorigenesis of prostate cancer cells via the STAT3/ NR4A3 axis. Epigenomics 2021; 13:1591-1605. [PMID: 34657447 DOI: 10.2217/epi-2021-0293] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aim: To explore the role and mechanism of long noncoding RNA AC245100.4 and NR4A3 in prostate cancer (PCa). Methods: RNA-sequencing analysis was used to detect the downstream genes of AC245100.4. A series of gain- and loss-of-function approaches were used to investigate the roles of AC245100.4 and NR4A3. RNA immunoprecipitation was performed to examine the interaction between AC245100.4 and STAT3. Results: AC245100.4 was significantly upregulated in PCa cells and tissues. Knockdown of AC21500.4 significantly inhibited the tumorigenesis of PCa cells. Mechanistically, AC245100.4 deregulated the transcription of NR4A3 via increasing p-STAT3, which acted as a transcriptional repressor of NR4A3. Conclusion: Knockdown of long noncoding RNA AC245100.4 inhibits the tumorigenesis of PCa cells via the STAT3/NR4A3 axis.
Collapse
Affiliation(s)
- Chi Liu
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China
| | - Ping Lin
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China
| | - Jiabin Zhao
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China.,Department of Emergency Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hui Xie
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China.,Teaching Experiment Center of Biotechnology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Rou Li
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China
| | - Xu Yang
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China
| | - Nan Wang
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China
| | - Huizhen Jia
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China
| | - Shan Jiang
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China
| | - Ke Zhang
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China
| | - Xiaoguang Yu
- Department of Biochemistry & Molecular Biology, Harbin Medical University, Harbin, Heilongjiang, 150086, China
| |
Collapse
|
14
|
Blasiak J, Hyttinen JMT, Szczepanska J, Pawlowska E, Kaarniranta K. Potential of Long Non-Coding RNAs in Age-Related Macular Degeneration. Int J Mol Sci 2021; 22:9178. [PMID: 34502084 PMCID: PMC8431062 DOI: 10.3390/ijms22179178] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/16/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022] Open
Abstract
Age-related macular degeneration (AMD) is the leading cause of visual impairment in the aging population with poorly known pathogenesis and lack of effective treatment. Age and family history are the strongest AMD risk factors, and several loci were identified to contribute to AMD. Recently, also the epigenetic profile was associated with AMD, and some long non-coding RNAs (lncRNAs) were shown to involve in AMD pathogenesis. The Vax2os1/2 (ventral anterior homeobox 2 opposite strand isoform 1) lncRNAs may modulate the balance between pro- and anti-angiogenic factors in the eye contributing to wet AMD. The stress-induced dedifferentiation of retinal pigment epithelium cells can be inhibited by the ZNF503-AS1 (zinc finger protein 503 antisense RNA 2) and LINC00167 lncRNAs. Overexpression of the PWRN2 (Prader-Willi region non-protein-coding RNA 2) lncRNA aggravated RPE cells apoptosis and mitochondrial impairment induced by oxidative stress. Several other lncRNAs were reported to exert protective or detrimental effects in AMD. However, many studies are limited to an association between lncRNA and AMD in patients or model systems with bioinformatics. Therefore, further works on lncRNAs in AMD are rational, and they should be enriched with mechanistic and clinical studies to validate conclusions obtained in high-throughput in vitro research.
Collapse
Affiliation(s)
- Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Juha M. T. Hyttinen
- Department of Ophthalmology, University of Eastern Finland, 70210 Kuopio, Finland;
| | - Joanna Szczepanska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland;
| | - Elzbieta Pawlowska
- Department of Orthodontics, Medical University of Lodz, 92-217 Lodz, Poland;
| | - Kai Kaarniranta
- Department of Ophthalmology, University of Eastern Finland, 70210 Kuopio, Finland;
- Department of Ophthalmology, Kuopio University Hospital, 70210 Kuopio, Finland
| |
Collapse
|
15
|
Wang M, Chen D, Zheng H, Zhao L, Xue X, Yu F, Zhang Y, Cheng C, Niu Q, Wang S, Zhang Y, Wu L. Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs. Front Cell Dev Biol 2021; 9:690167. [PMID: 34422813 PMCID: PMC8377728 DOI: 10.3389/fcell.2021.690167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Embryonic development depends on a highly coordinated shift in transcription programs known as the maternal-to-zygotic transition (MZT). It remains unclear how haploid and diploid embryo coordinate their genomic activation and embryonic development during MZT in haplodiploid animals. Here, we applied a single-embryo RNA-seq approach to characterize the embryonic transcriptome dynamics in haploid males vs. diploid females of the haplodiploid insect honeybee (Apis mellifera). We observed typical zygotic genome activation (ZGA) occurred in three major waves specifically in female honeybee embryos; haploid genome activation was much weaker and occurred later. Strikingly, we also observed three waves of transcriptional activation for thousands of long non-coding transcripts (lncRNA), 73% of which are transcribed from intronic regions and 65% were specific to female honeybee embryos. These findings support a model in which introns encode thousands of lncRNAs that are expressed in a diploid-embryo-specific and ZGA-triggered manner that may have potential functions to regulate gene expression during early embryonic development in the haplodiploid insect honeybee.
Collapse
Affiliation(s)
- Miao Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Huoqing Zheng
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Liuwei Zhao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofeng Xue
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengyun Yu
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Yu Zhang
- ABLife BioBigData Institute, Wuhan, China
| | - Chao Cheng
- ABLife BioBigData Institute, Wuhan, China
| | - Qingsheng Niu
- Department of Scientific Research, Jilin Province Institute of Apicultural Science, Jilin, China
| | - Shuai Wang
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Liming Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
16
|
Capturing Endogenous Long Noncoding RNAs and Their Binding Proteins Using Chromatin Isolation by RNA Purification. Methods Mol Biol 2021. [PMID: 34417745 DOI: 10.1007/978-1-0716-1697-0_9] [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] [Indexed: 12/18/2023]
Abstract
Long noncoding RNAs (lncRNAs) exert their functions through binding to other RNA, genomic DNA, or proteins. The identification of proteins that associate with the lncRNA of interest sheds light on the molecular basis of its biological functions. This can be achieved by tagging the lncRNA with chemically modified ribonucleotides, or by using in vitro transcribed lncRNA to retrieve proteins from cell lysates. Alternatively, endogenous lncRNAs can be pulled down from cells or tissues with biotinylated antisense DNA oligonucleotides, which may overcome the potential pitfalls of using tagged lncRNAs, such as artifacts caused by tagging or non-physiological interactions. Here we describe the detailed protocol for chromatin isolation by RNA purification (ChIRP) from mammalian cell lines and mouse tissues, which captures endogenous lncRNAs and enables subsequent identification of their physiologically relevant binding partners.
Collapse
|
17
|
Building Pluripotency Identity in the Early Embryo and Derived Stem Cells. Cells 2021; 10:cells10082049. [PMID: 34440818 PMCID: PMC8391114 DOI: 10.3390/cells10082049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
The fusion of two highly differentiated cells, an oocyte with a spermatozoon, gives rise to the zygote, a single totipotent cell, which has the capability to develop into a complete, fully functional organism. Then, as development proceeds, a series of programmed cell divisions occur whereby the arising cells progressively acquire their own cellular and molecular identity, and totipotency narrows until when pluripotency is achieved. The path towards pluripotency involves transcriptome modulation, remodeling of the chromatin epigenetic landscape to which external modulators contribute. Both human and mouse embryos are a source of different types of pluripotent stem cells whose characteristics can be captured and maintained in vitro. The main aim of this review is to address the cellular properties and the molecular signature of the emerging cells during mouse and human early development, highlighting similarities and differences between the two species and between the embryos and their cognate stem cells.
Collapse
|
18
|
Exploring chromatin structural roles of non-coding RNAs at imprinted domains. Biochem Soc Trans 2021; 49:1867-1879. [PMID: 34338292 PMCID: PMC8421051 DOI: 10.1042/bst20210758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/11/2022]
Abstract
Different classes of non-coding RNA (ncRNA) influence the organization of chromatin. Imprinted gene domains constitute a paradigm for exploring functional long ncRNAs (lncRNAs). Almost all express an lncRNA in a parent-of-origin dependent manner. The mono-allelic expression of these lncRNAs represses close by and distant protein-coding genes, through diverse mechanisms. Some control genes on other chromosomes as well. Interestingly, several imprinted chromosomal domains show a developmentally regulated, chromatin-based mechanism of imprinting with apparent similarities to X-chromosome inactivation. At these domains, the mono-allelic lncRNAs show a relatively stable, focal accumulation in cis. This facilitates the recruitment of Polycomb repressive complexes, lysine methyltranferases and other nuclear proteins — in part through direct RNA–protein interactions. Recent chromosome conformation capture and microscopy studies indicate that the focal aggregation of lncRNA and interacting proteins could play an architectural role as well, and correlates with close positioning of target genes. Higher-order chromatin structure is strongly influenced by CTCF/cohesin complexes, whose allelic association patterns and actions may be influenced by lncRNAs as well. Here, we review the gene-repressive roles of imprinted non-coding RNAs, particularly of lncRNAs, and discuss emerging links with chromatin architecture.
Collapse
|
19
|
Policarpo R, Sierksma A, De Strooper B, d'Ydewalle C. From Junk to Function: LncRNAs in CNS Health and Disease. Front Mol Neurosci 2021; 14:714768. [PMID: 34349622 PMCID: PMC8327212 DOI: 10.3389/fnmol.2021.714768] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/25/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in RNA sequencing technologies helped to uncover the existence of tens of thousands of long non-coding RNAs (lncRNAs) that arise from the dark matter of the genome. These lncRNAs were originally thought to be transcriptional noise but an increasing number of studies demonstrate that these transcripts can modulate protein-coding gene expression by a wide variety of transcriptional and post-transcriptional mechanisms. The spatiotemporal regulation of lncRNA expression is particularly evident in the central nervous system, suggesting that they may directly contribute to specific brain processes, including neurogenesis and cellular homeostasis. Not surprisingly, lncRNAs are therefore gaining attention as putative novel therapeutic targets for disorders of the brain. In this review, we summarize the recent insights into the functions of lncRNAs in the brain, their role in neuronal maintenance, and their potential contribution to disease. We conclude this review by postulating how these RNA molecules can be targeted for the treatment of yet incurable neurological disorders.
Collapse
Affiliation(s)
- Rafaela Policarpo
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Annerieke Sierksma
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,UK Dementia Research Institute, University College London, London, United Kingdom
| | - Constantin d'Ydewalle
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| |
Collapse
|
20
|
Abstract
Diabetic retinopathy (DR), which is known as a severe complication of type 2 diabetes mellitus, can cause varying degrees of damage to visual acuity. The pathogenesis of DR is multifactorial and not fully understood. Many previous research studies have revealed that an aberrant level of some long non-coding RNAs (lncRNAs) may accelerate the development of DR. These lncRNAs are regulatory factors and research related to them is always underway. In this review, we will update several types of lncRNAs based on the previous studies which are related to the development of DR and discuss its potential mechanisms of action and connections. Generally, the review will help us know more about lncRNAs and provide directions for future research related to DR.
Collapse
Affiliation(s)
- Qinying Huang
- Shantou University Medical College, Shantou, Guangdong, China
- Department of Ophthalmology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Jinying Li
- Department of Ophthalmology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Mutzel V, Schulz EG. Dosage Sensing, Threshold Responses, and Epigenetic Memory: A Systems Biology Perspective on Random X-Chromosome Inactivation. Bioessays 2021; 42:e1900163. [PMID: 32189388 DOI: 10.1002/bies.201900163] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/27/2020] [Indexed: 02/06/2023]
Abstract
X-chromosome inactivation ensures dosage compensation between the sexes in mammals by randomly choosing one out of the two X chromosomes in females for inactivation. This process imposes a plethora of questions: How do cells count their X chromosome number and ensure that exactly one stays active? How do they randomly choose one of two identical X chromosomes for inactivation? And how do they stably maintain this state of monoallelic expression? Here, different regulatory concepts and their plausibility are evaluated in the context of theoretical studies that have investigated threshold behavior, ultrasensitivity, and bistability through mathematical modeling. It is discussed how a twofold difference between a single and a double dose of X-linked genes might be converted to an all-or-nothing response and how mutually exclusive expression can be initiated and maintained. Finally, candidate factors that might mediate the proposed regulatory principles are reviewed.
Collapse
Affiliation(s)
- Verena Mutzel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| |
Collapse
|
23
|
Grigoryan A, Pospiech J, Krämer S, Lipka D, Liehr T, Geiger H, Kimura H, Mulaw MA, Florian MC. Attrition of X Chromosome Inactivation in Aged Hematopoietic Stem Cells. Stem Cell Reports 2021; 16:708-716. [PMID: 33798450 PMCID: PMC8072063 DOI: 10.1016/j.stemcr.2021.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 01/03/2023] Open
Abstract
During X chromosome inactivation (XCI), the inactive X chromosome (Xi) is recruited to the nuclear lamina at the nuclear periphery. Beside X chromosome reactivation resulting in a highly penetrant aging-like hematopoietic malignancy, little is known about XCI in aged hematopoietic stem cells (HSCs). Here, we demonstrate that LaminA/C defines a distinct repressive nuclear compartment for XCI in young HSCs, and its reduction in aged HSCs correlates with an impairment in the overall control of XCI. Integrated omics analyses reveal higher variation in gene expression, global hypomethylation, and significantly increased chromatin accessibility on the X chromosome (Chr X) in aged HSCs. In summary, our data support the role of LaminA/C in the establishment of a special repressive compartment for XCI in HSCs, which is impaired upon aging.
Collapse
Affiliation(s)
- Ani Grigoryan
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany
| | - Johannes Pospiech
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany
| | - Stephen Krämer
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany; Bioinformatics and Omics Data Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany; Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Daniel Lipka
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, 07747 Jena, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Medhanie A Mulaw
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany; Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany.
| | - Maria Carolina Florian
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany; Stem Cell Aging Group, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], Av. Gran Via 199-203, 08908, L'Hospitalet de Llobregat, Barcelona, Spain; Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.
| |
Collapse
|
24
|
Cheng T, Huang S. Roles of Non-Coding RNAs in Cervical Cancer Metastasis. Front Oncol 2021; 11:646192. [PMID: 33777808 PMCID: PMC7990873 DOI: 10.3389/fonc.2021.646192] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 02/03/2021] [Indexed: 12/24/2022] Open
Abstract
Metastasis remains to be a huge challenge in cancer therapy. The mechanism underlying cervical cancer metastasis is not well understood and needs to be elucidated. Recent studies have highlighted the diverse roles of non-coding RNAs in cancer progression and metastasis. Increasing numbers of miRNAs, lncRNAs and circRNAs are found to be dysregulated in cervical cancer, associated with metastasis. They have been shown to regulate metastasis through regulating metastasis-related genes, epithelial-mesenchymal transition, signaling pathways and interactions with tumor microenvironment. Moreover, miRNAs can interact with lncRNAs and circRNAs respectively during this complex process. Herein, we review literatures up to date involving non-coding RNAs in cervical cancer metastasis, mainly focus on the underlying mechanisms and highlight the interaction network between miRNAs and lncRNAs, as well as circRNAs. Finally, we discuss the therapeutic prospects.
Collapse
Affiliation(s)
- Tanchun Cheng
- Department of Obstetrics and Gynecology, Affiliated Haikou Hospital, Xiangya Medical College of Central South University, Haikou, China
| | - Shouguo Huang
- Department of Obstetrics and Gynecology, Affiliated Haikou Hospital, Xiangya Medical College of Central South University, Haikou, China
| |
Collapse
|
25
|
Pachera E, Assassi S, Salazar GA, Stellato M, Renoux F, Wunderlin A, Blyszczuk P, Lafyatis R, Kurreeman F, de Vries-Bouwstra J, Messemaker T, Feghali-Bostwick CA, Rogler G, van Haaften WT, Dijkstra G, Oakley F, Calcagni M, Schniering J, Maurer B, Distler JH, Kania G, Frank-Bertoncelj M, Distler O. Long noncoding RNA H19X is a key mediator of TGF-β-driven fibrosis. J Clin Invest 2021; 130:4888-4905. [PMID: 32603313 DOI: 10.1172/jci135439] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/17/2020] [Indexed: 12/22/2022] Open
Abstract
TGF-β is a master regulator of fibrosis, driving the differentiation of fibroblasts into apoptosis-resistant myofibroblasts and sustaining the production of extracellular matrix (ECM) components. Here, we identified the nuclear long noncoding RNA (lncRNA) H19X as a master regulator of TGF-β-driven tissue fibrosis. H19X was consistently upregulated in a wide variety of human fibrotic tissues and diseases and was strongly induced by TGF-β, particularly in fibroblasts and fibroblast-related cells. Functional experiments following H19X silencing revealed that H19X was an obligatory factor for TGF-β-induced ECM synthesis as well as differentiation and survival of ECM-producing myofibroblasts. We showed that H19X regulates DDIT4L gene expression, specifically interacting with a region upstream of the DDIT4L gene and changing the chromatin accessibility of a DDIT4L enhancer. These events resulted in transcriptional repression of DDIT4L and, in turn, in increased collagen expression and fibrosis. Our results shed light on key effectors of TGF-β-induced ECM remodeling and fibrosis.
Collapse
Affiliation(s)
- Elena Pachera
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Shervin Assassi
- Division of Rheumatology, Department of Internal Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, USA
| | - Gloria A Salazar
- Division of Rheumatology, Department of Internal Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, USA
| | - Mara Stellato
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Florian Renoux
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Adam Wunderlin
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Przemyslaw Blyszczuk
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Tobias Messemaker
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Wouter T van Haaften
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, Netherlands
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maurizio Calcagni
- Department of Plastic Surgery and Hand Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Janine Schniering
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Britta Maurer
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Jörg Hw Distler
- Department of Internal Medicine 3, University of Erlangen, Erlangen, Germany
| | - Gabriela Kania
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Mojca Frank-Bertoncelj
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| |
Collapse
|
26
|
Ashrafizadeh M, Gholami MH, Mirzaei S, Zabolian A, Haddadi A, Farahani MV, Kashani SH, Hushmandi K, Najafi M, Zarrabi A, Ahn KS, Khan H. Dual relationship between long non-coding RNAs and STAT3 signaling in different cancers: New insight to proliferation and metastasis. Life Sci 2021; 270:119006. [PMID: 33421521 DOI: 10.1016/j.lfs.2020.119006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022]
Abstract
Uncontrolled growth and metastasis of cancer cells is an increasing challenge for overcoming cancer, and improving survival of patients. Complicated signaling networks account for proliferation and invasion of cancer cells that need to be elucidated for providing effective cancer therapy, and minimizing their malignancy. Long non-coding RNAs (lncRNAs) are RNA molecules with a length of more than 200 nucleotides. They participate in cellular events, and their dysregulation in a common phenomenon in different cancers. Noteworthy, lncRNAs can regulate different molecular pathways, and signal transducer and activator of transcription 3 (STAT3) is one of them. STAT3 is a tumor-promoting factors in cancers due to its role in cancer proliferation (cell cycle progression and apoptosis inhibition) and metastasis (EMT induction). LncRNAs can function as upstream mediators of STAT3 pathway, reducing/enhancing its expression. This dual relationship is of importance in affecting proliferation and metastasis of cancer cells. The response of cancer cells to therapy such as chemotherapy and radiotherapy is regulated by lncRNA/STAT3 axis. Tumor-promoting lncRNAs including NEAT1, SNHG3 and H19 induces STAT3 expression, while tumor-suppressing lncRNAs such as MEG3, PTCSC3 and NKILA down-regulate STAT3 expression. Noteworthy, upstream mediators of STAT3 such as microRNAs can be regulated by lncRNAs. These complicated signaling networks are mechanistically described in the current review.
Collapse
Affiliation(s)
- Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla 34956, Istanbul, Turkey; Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla 34956, Istanbul, Turkey
| | | | - Sepideh Mirzaei
- Department of Biology, Faculty of Science, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Amirhossein Zabolian
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Amirabbas Haddadi
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | | | | | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Masoud Najafi
- Medical Technology Research Center, Institute of Health Technology, Kermanshah University of Medical Sciences, Kermanshah 6715847141, Iran; Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla 34956, Istanbul, Turkey.
| | - Kwang Seok Ahn
- Department of Science in Korean Medicine, Kyung Hee University, 24 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Republic of Korea.
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan 23200, Pakistan.
| |
Collapse
|
27
|
RNA-Centric Methods: Toward the Interactome of Specific RNA Transcripts. Trends Biotechnol 2020; 39:890-900. [PMID: 33353763 DOI: 10.1016/j.tibtech.2020.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022]
Abstract
RNA-protein interactions play an important role in numerous cellular processes in health and disease. In recent years, the global RNA-bound proteome has been extensively studied, uncovering many previously unknown RNA-binding proteins. However, little is known about which particular proteins bind to which specific RNA transcript. In this review, we provide an overview of methods to identify RNA-protein interactions, with a particular focus on strategies that provide insights into the interactome of specific RNA transcripts. Finally, we discuss challenges and future directions, including the potential of CRISPR-RNA targeting systems to investigate endogenous RNA-protein interactions.
Collapse
|
28
|
Panda A, Zylicz JJ, Pasque V. New Insights into X-Chromosome Reactivation during Reprogramming to Pluripotency. Cells 2020; 9:E2706. [PMID: 33348832 PMCID: PMC7766869 DOI: 10.3390/cells9122706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Dosage compensation between the sexes results in one X chromosome being inactivated during female mammalian development. Chromosome-wide transcriptional silencing from the inactive X chromosome (Xi) in mammalian cells is erased in a process termed X-chromosome reactivation (XCR), which has emerged as a paradigm for studying the reversal of chromatin silencing. XCR is linked with germline development and induction of naive pluripotency in the epiblast, and also takes place upon reprogramming somatic cells to induced pluripotency. XCR depends on silencing of the long non-coding RNA (lncRNA) X inactive specific transcript (Xist) and is linked with the erasure of chromatin silencing. Over the past years, the advent of transcriptomics and epigenomics has provided new insights into the transcriptional and chromatin dynamics with which XCR takes place. However, multiple questions remain unanswered about how chromatin and transcription related processes enable XCR. Here, we review recent work on establishing the transcriptional and chromatin kinetics of XCR, as well as discuss a model by which transcription factors mediate XCR not only via Xist repression, but also by direct targeting of X-linked genes.
Collapse
Affiliation(s)
- Amitesh Panda
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
| | - Jan J. Zylicz
- The Novo Nordisk Foundation Center for Stem Cell Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Vincent Pasque
- Laboratory of Cellular Reprogramming and Epigenetic Regulation, Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven-University of Leuven, 3000 Leuven, Belgium;
| |
Collapse
|
29
|
Yan Q, Shields EJ, Bonasio R, Sarma K. Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach. Cell Rep 2020; 29:1369-1380.e5. [PMID: 31665646 PMCID: PMC6870988 DOI: 10.1016/j.celrep.2019.09.052] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022] Open
Abstract
R-loops are three-stranded DNA:RNA hybrids that are implicated in many nuclear processes. While R-loops may have physiological roles, the formation of stable, aberrant R-loops has been observed in neurological disorders and cancers. Current methods to assess their genome-wide distribution rely on affinity purification, which is plagued by large input requirements, high noise, and poor sensitivity for dynamic R-loops. Here, we present MapR, a method that utilizes RNase H to guide micrococcal nuclease to R-loops, which are subsequently cleaved, released, and identified by sequencing. MapR detects R-loops formed at promoters and active enhancers that are likely to form transient R-loops due to the low transcriptional output of these regulatory elements and the short-lived nature of enhancer RNAs. MapR is as specific as existing techniques and more sensitive, allowing for genomewide coverage with low input material in a fraction of the time. Yan et al. report a fast, easy, antibodyindependent strategy, MapR, to identify native R-loops in vivo without the need for generating stable cell lines. MapR uses the natural affinity and specificity of RNase H to detect R-loops. MapR identifies dynamic R-loops formed at enhancers with high sensitivity.
Collapse
Affiliation(s)
- Qingqing Yan
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily J Shields
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
30
|
Müller M, Schauer T, Krause S, Villa R, Thomae AW, Becker PB. Two-step mechanism for selective incorporation of lncRNA into a chromatin modifier. Nucleic Acids Res 2020; 48:7483-7501. [PMID: 32510132 PMCID: PMC7528653 DOI: 10.1093/nar/gkaa492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 02/04/2023] Open
Abstract
The MLE DExH helicase and the roX lncRNAs are essential components of the chromatin modifying Dosage Compensation Complex (DCC) in Drosophila. To explore the mechanism of ribonucleoprotein complex assembly, we developed vitRIP, an unbiased, transcriptome-wide in vitro assay that reveals RNA binding specificity. We found that MLE has intrinsic specificity for U-/A-rich sequences and tandem stem-loop structures and binds many RNAs beyond roX in vitro. The selectivity of the helicase for physiological substrates is further enhanced by the core DCC. Unwinding of roX2 by MLE induces a highly selective RNA binding surface in the unstructured C-terminus of the MSL2 subunit and triggers-specific association of MLE and roX2 with the core DCC. The exquisite selectivity of roX2 incorporation into the DCC thus originates from intimate cooperation between the helicase and the core DCC involving two distinct RNA selection principles and their mutual refinement.
Collapse
Affiliation(s)
- Marisa Müller
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Tamas Schauer
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Silke Krause
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Raffaella Villa
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas W Thomae
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Core Facility Bioimaging at the Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
31
|
Kimura T. [Non-coding Natural Antisense RNA: Mechanisms of Action in the Regulation of Target Gene Expression and Its Clinical Implications]. YAKUGAKU ZASSHI 2020; 140:687-700. [PMID: 32378673 DOI: 10.1248/yakushi.20-00002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent advances in high-throughput technologies have revealed that 75% of the human genome is transcribed to RNA, whereas only 3% of transcripts are translated into proteins. Consequently, many long non-coding RNAs (lncRNAs) have been identified, which has improved our understanding of the complexity of biological processes. LncRNAs comprise multiple classes of RNA transcripts that regulate the transcription, stability and translation of protein-coding genes in a genome. Natural antisense transcripts (NATs) form one such class, and the GENCODE v30 catalog contains 16193 lncRNA loci, of which 5611 are antisense loci. This review outlines our emerging understanding of lncRNAs, with a particular focus on how lncRNAs regulate gene expression using interferon-α1 (IFN-α1) mRNA and its antisense partner IFN-α1 antisense (as)RNA as an example. We have identified and characterized the asRNA that determines post-transcriptional IFN-α1 mRNA levels. IFN-α1 asRNA stabilizes IFN-α1 mRNA by cytoplasmic sense-antisense duplex formation, which may enhance the accessibility of an RNA stabilizer protein or decrease the affinity of an RNA decay factor for the RNA. IFN-α1 asRNA can also act as competing molecules in the competing endogenous (ce)RNA network with other members of the IFNA multigene family mRNAs/asRNAs, and other cellular mRNA transcripts. Furthermore, antisense oligoribonucleotides representing functional domains of IFN-α1 asRNA inhibit influenza virus proliferation in the respiratory tract of virus-infected animals. Thus, these findings support, at least in part, the rationale that dissecting the activity of NAT on gene expression regulation promises to reveal previously unanticipated biology, with potential to provide new therapeutic approaches to diseases.
Collapse
Affiliation(s)
- Tominori Kimura
- Laboratory of Microbiology and Cell Biology, Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University
| |
Collapse
|
32
|
Jones AN, Sattler M. Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats. J Mol Cell Biol 2020; 11:845-859. [PMID: 31336384 PMCID: PMC6917512 DOI: 10.1093/jmcb/mjz086] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Following the discovery of numerous long non-coding RNA (lncRNA) transcripts in the human genome, their important roles in biology and human disease are emerging. Recent progress in experimental methods has enabled the identification of structural features of lncRNAs. However, determining high-resolution structures is challenging as lncRNAs are expected to be dynamic and adopt multiple conformations, which may be modulated by interaction with protein binding partners. The X-inactive specific transcript (Xist) is necessary for X inactivation during dosage compensation in female placental mammals and one of the best-studied lncRNAs. Recent progress has provided new insights into the domain organization, molecular features, and RNA binding proteins that interact with distinct regions of Xist. The A-repeats located at the 5′ end of the transcript are of particular interest as they are essential for mediating silencing of the inactive X chromosome. Here, we discuss recent progress with elucidating structural features of the Xist lncRNA, focusing on the A-repeats. We discuss the experimental and computational approaches employed that have led to distinct structural models, likely reflecting the intrinsic dynamics of this RNA. The presence of multiple dynamic conformations may also play an important role in the formation of the associated RNPs, thus influencing the molecular mechanism underlying the biological function of the Xist A-repeats. We propose that integrative approaches that combine biochemical experiments and high-resolution structural biology in vitro with chemical probing and functional studies in vivo are required to unravel the molecular mechanisms of lncRNAs.
Collapse
Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Center for Integrated Protein Science Munich and Bavarian NMR Center at Department of Chemistry, Technical University of Munich, Garching, 85747, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Center for Integrated Protein Science Munich and Bavarian NMR Center at Department of Chemistry, Technical University of Munich, Garching, 85747, Germany
| |
Collapse
|
33
|
Miguel V, Lamas S, Espinosa-Diez C. Role of non-coding-RNAs in response to environmental stressors and consequences on human health. Redox Biol 2020; 37:101580. [PMID: 32723695 PMCID: PMC7767735 DOI: 10.1016/j.redox.2020.101580] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022] Open
Abstract
Environmental risk factors, including physicochemical agents, noise and mental stress, have a considerable impact on human health. This environmental exposure may lead to epigenetic reprogramming, including changes in non-coding RNAs (ncRNAs) signatures, which can contribute to the pathophysiology state. Oxidative stress is one of the results of this environmental disturbance by modifying cellular processes such as apoptosis, signal transduction cascades, and DNA repair mechanisms. In this review, we delineate environmental risk factors and their influence on (ncRNAs) in connection to disease. We focus on well-studied miRNAs and analyze the novel roles of long-non-coding-RNAs (lncRNAs). We discuss commonly regulated lncRNAs after exposure to different stressors, such as UV, heavy metals and pesticides among others, and the potential role of these lncRNA as exposure biomarkers, epigenetic regulators and potential therapeutic targets to diminish the deleterious secondary response to environmental agents. Environmental stressors induce epigenetic changes that lead to long-lasting gene expression changes and pathology development. NcRNAs, miRNAs and lncRNAs, are epigenetic modifiers susceptible to changes in expression after environmental insults . LncRNAs influence cell function partnering with other biomolecules such as proteins, DNA, RNA or other ncRNAs. LncRNA dysregulation affects cell development, carcinogenesis, vascular disease and neurodegenerative disorders. ncRNA signatures can be potentially used as biomarkers to identify exposure to specific environmental stressors.
Collapse
Affiliation(s)
- Verónica Miguel
- Programme of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Santiago Lamas
- Programme of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Cristina Espinosa-Diez
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, PA, USA.
| |
Collapse
|
34
|
Abstract
Long non-coding RNA (lncRNA) Xist has emerged as a key modulator in dosage compensation by randomly inactivating one of the X chromosomes in mammals during embryonic development. Dysregulation of X chromosome inactivation (XCI) due to deletion of Xist has been proven to induce hematologic cancer in mice. However, this phenomenon is not consistent in humans as growing evidence suggests Xist can suppress or promote cancer growth in different organs of the human body. In this review, we discuss recent advances of XCI in human embryonic stem cells and provide an explanation for the seemingly contradictory roles of Xist in development of human cancer.
Collapse
Affiliation(s)
- Yung-Kang Chen
- School of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of General Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yun Yen
- Graduate Institute of Medical Informatics, Taipei Medical University, Taipei, Taiwan. .,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, 250 Wuxing Street, Taipei City, 110, Taiwan. .,Taipei Municipal Wanfang Hospital, Taipei Medical University, Taipei, Taiwan. .,Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
| |
Collapse
|
35
|
Żylicz JJ, Heard E. Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective. Annu Rev Biochem 2020; 89:255-282. [PMID: 32259458 DOI: 10.1146/annurev-biochem-062917-012655] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Facultative heterochromatin (fHC) concerns the developmentally regulated heterochromatinization of different regions of the genome and, in the case of the mammalian X chromosome and imprinted loci, of only one allele of a homologous pair. The formation of fHC participates in the timely repression of genes, by resisting strong trans activators. In this review, we discuss the molecular mechanisms underlying the establishment and maintenance of fHC in mammals using a mouse model. We focus on X-chromosome inactivation (XCI) as a paradigm for fHC but also relate it to genomic imprinting and homeobox (Hox) gene cluster repression. A vital role for noncoding transcription and/or transcripts emerges as the general principle of triggering XCI and canonical imprinting. However, other types of fHC are established through an unknown mechanism, independent of noncoding transcription (Hox clusters and noncanonical imprinting). We also extensively discuss polycomb-group repressive complexes (PRCs), which frequently play a vital role in fHC maintenance.
Collapse
Affiliation(s)
- Jan J Żylicz
- Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR 3215, INSERM U934, PSL University, 75248 Paris Cedex 05, France.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, United Kingdom
| | - Edith Heard
- Directors' Research, EMBL Heidelberg, 69117 Heidelberg, Germany;
| |
Collapse
|
36
|
An Overview of Non-coding RNAs and Cardiovascular System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:3-45. [PMID: 32285403 DOI: 10.1007/978-981-15-1671-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cardiovascular disease management and timely diagnosis remain a major dilemma. Delineating molecular mechanisms of cardiovascular diseases is opening horizon in the field of molecular medicines and in the development of early diagnostic markers. Non-coding RNAs are the highly functional and vibrant nucleic acids and are known to be involved in the regulation of endothelial cells, vascular and smooth muscles cells, cardiac metabolism, ischemia, inflammation and many processes in cardiovascular system. This chapter is comprehensively focusing on the overview of the non-coding RNAs including their discovery, generation, classification and functional regulation. In addition, overview regarding different non-coding RNAs as long non-coding, siRNAs and miRNAs involvement in the cardiovascular diseases is also addressed. Detailed functional analysis of this vast group of highly regulatory molecules will be promising for shaping future drug discoveries.
Collapse
|
37
|
Ala U. Competing Endogenous RNAs, Non-Coding RNAs and Diseases: An Intertwined Story. Cells 2020; 9:E1574. [PMID: 32605220 PMCID: PMC7407898 DOI: 10.3390/cells9071574] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 01/17/2023] Open
Abstract
MicroRNAs (miRNAs), a class of small non-coding RNA molecules, are responsible for RNA silencing and post-transcriptional regulation of gene expression. They can mediate a fine-tuned crosstalk among coding and non-coding RNA molecules sharing miRNA response elements (MREs). In a suitable environment, both coding and non-coding RNA molecules can be targeted by the same miRNAs and can indirectly regulate each other by competing for them. These RNAs, otherwise known as competing endogenous RNAs (ceRNAs), lead to an additional post-transcriptional regulatory layer, where non-coding RNAs can find new significance. The miRNA-mediated interplay among different types of RNA molecules has been observed in many different contexts. The analyses of ceRNA networks in cancer and other pathologies, as well as in other physiological conditions, provide new opportunities for interpreting omics data for the field of personalized medicine. The development of novel computational tools, providing putative predictions of ceRNA interactions, is a rapidly growing field of interest. In this review, I discuss and present the current knowledge of the ceRNA mechanism and its implications in a broad spectrum of different pathologies, such as cardiovascular or autoimmune diseases, cancers and neurodegenerative disorders.
Collapse
Affiliation(s)
- Ugo Ala
- Department of Veterinary Sciences, University of Turin, 10124 Turin, Italy
| |
Collapse
|
38
|
Kato M, Carninci P. Genome-Wide Technologies to Study RNA-Chromatin Interactions. Noncoding RNA 2020; 6:ncrna6020020. [PMID: 32471183 PMCID: PMC7345514 DOI: 10.3390/ncrna6020020] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 12/21/2022] Open
Abstract
An increasing number of studies have revealed that long non-coding RNAs (lncRNAs) play important roles in gene regulation and nuclear organization. Although the mechanisms are still largely unknown, many lncRNAs have been shown to interact with chromatin. Thus, one approach to understanding the function of these lncRNAs is to identify their sites of genomic interaction. Hybridization capture methods using oligonucleotide probes have been used for years to study chromatin-associated RNA. Recently, several groups have developed novel methods based on proximity ligation to investigate RNA–chromatin interactions at a genome-wide scale. This review discusses these technologies and highlights their advantages and disadvantages for the consideration of potential users.
Collapse
Affiliation(s)
- Masaki Kato
- Correspondence: (M.K.); (P.C.); Tel.: +81-045-503-9111 (M.K.)
| | - Piero Carninci
- Correspondence: (M.K.); (P.C.); Tel.: +81-045-503-9111 (M.K.)
| |
Collapse
|
39
|
Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function. Nat Commun 2020; 11:2219. [PMID: 32376827 PMCID: PMC7203109 DOI: 10.1038/s41467-020-15902-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 03/27/2020] [Indexed: 01/01/2023] Open
Abstract
Heterochromatin in the eukaryotic genome is rigorously controlled by the concerted action of protein factors and RNAs. Here, we investigate the RNA binding function of ATRX, a chromatin remodeler with roles in silencing of repetitive regions of the genome and in recruitment of the polycomb repressive complex 2 (PRC2). We identify ATRX RNA binding regions (RBRs) and discover that the major ATRX RBR lies within the N-terminal region of the protein, distinct from its PHD and helicase domains. Deletion of this ATRX RBR (ATRXΔRBR) compromises ATRX interactions with RNAs in vitro and in vivo and alters its chromatin binding properties. Genome-wide studies reveal that loss of RNA interactions results in a redistribution of ATRX on chromatin. Finally, our studies identify a role for ATRX-RNA interactions in regulating PRC2 localization to a subset of polycomb target genes. ATRX is an RNA binding protein that mediates targeting of polycomb repressive complex 2 (PRC2) to genomic sites. Here the authors identify the RNA binding region and show that the RNA binding is required for ATRX localization and for its recruitment of PRC2 to a subset of polycomb targets.
Collapse
|
40
|
Long non-coding RNA XIST regulates hyperglycemia-associated apoptosis and migration in human retinal pigment epithelial cells. Biomed Pharmacother 2020; 125:109959. [DOI: 10.1016/j.biopha.2020.109959] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/20/2020] [Accepted: 01/23/2020] [Indexed: 11/27/2022] Open
|
41
|
Gao J, Wang F, Wu P, Chen Y, Jia Y. Aberrant LncRNA Expression in Leukemia. J Cancer 2020; 11:4284-4296. [PMID: 32368311 PMCID: PMC7196264 DOI: 10.7150/jca.42093] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/31/2020] [Indexed: 02/05/2023] Open
Abstract
Leukemia is a common malignant cancer of the hematopoietic system, whose pathogenesis has not been fully elucidated. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides without protein-coding function. Recent studies report their role in cellular processes such as the regulation of gene expression, as well as in the carcinogenesis, occurrence, development, and prognosis of various tumors. Evidence indicating relationships between a variety of lncRNAs and leukemia pathophysiology has increased dramatically in the previous decade, with specific lncRNAs expected to serve as diagnostic biomarkers, novel therapeutic targets, and predictors of clinical outcomes. Furthermore, these lncRNAs might offer insight into disease pathogenesis and novel treatment options. This review summarizes progress in studies on the role(s) of lncRNAs in leukemia.
Collapse
Affiliation(s)
- Jie Gao
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Fujue Wang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Pengqiang Wu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yingying Chen
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yongqian Jia
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| |
Collapse
|
42
|
Luo Y, Yang J, Yu J, Liu X, Yu C, Hu J, Shi H, Ma X. Long Non-coding RNAs: Emerging Roles in the Immunosuppressive Tumor Microenvironment. Front Oncol 2020; 10:48. [PMID: 32083005 PMCID: PMC7005925 DOI: 10.3389/fonc.2020.00048] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/13/2020] [Indexed: 02/05/2023] Open
Abstract
Tumor immunosuppression may assist the immune escape of cancer cells, which promotes tumor metastasis and resistance to chemo-radiotherapy. The therapeutic strategies against tumor immunosuppression mainly focus on blocking immune checkpoint receptors, enhancing T-cell recognition and neutralizing inhibitory molecules. Although immunotherapies based on these strategies have improved the clinical outcomes, immunological nonresponse and resistance are two barriers to tumor eradication. Therefore, there is an urgent need to identify new biomarkers for patient selection and therapeutic targets for the development of combination regimen with immunotherapy. Recent studies have reported that non-protein-coding modulators exhibit important functions in post-transcriptional gene regulation, which subsequently modulates multiple pathophysiological processes, including neoplastic transformation. Differentiated from microRNAs, long non-coding RNAs (lncRNAs) are reported to be involved in various processes of the immune response in the tumor microenvironment (TME) to promote tumor immunosuppression. Currently, studies on tumor immunity regulated by lncRNAs are mainly confined to certain types of cancer cells or stromal cells. Additionally, the majority of studies are focused on the events involved in T cells and myeloid-derived suppressor cells (MDSCs). Although the reported studies have indicated the significance of lncRNAs in immunotherapy, the lack of comprehensive studies prevents us from exploring useful lncRNAs. In the current review, we have summarized the roles of lncRNAs in tumor immune response, and highlighted major lncRNAs as potential biomarkers or therapeutic targets for clinical application of immunotherapy.
Collapse
Affiliation(s)
- Ya Luo
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jiqiao Yang
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.,Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Yu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xiaowei Liu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Chune Yu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, China
| | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xuelei Ma
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.,State Key Laboratory of Biotherapy, Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
43
|
Wingett SW, Andrews S, Fraser P, Morf J. RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome. Sci Data 2020; 7:35. [PMID: 31992717 PMCID: PMC6987088 DOI: 10.1038/s41597-020-0372-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/09/2020] [Indexed: 11/09/2022] Open
Abstract
We have previously developed and described a method for measuring RNA co-locations within cells, called Proximity RNA-seq, which promises insights into RNA expression, processing, storage and translation. Here, we describe transcriptome-wide proximity RNA-seq datasets obtained from human neuroblastoma SH-SY5Y cell nuclei. To aid future users of this method, we also describe and release our analysis pipeline, CloseCall, which maps cDNA to a custom transcript annotation and allocates cDNA-linked barcodes to barcode groups. CloseCall then performs Monte Carlo simulations on the data to identify pairs of transcripts, which are co-barcoded more frequently than expected by chance. Furthermore, derived co-barcoding frequencies for individual transcripts, dubbed valency, serve as proxies for RNA density or connectivity for that given transcript. We outline how this pipeline was applied to these sequencing datasets and openly share the processed data outputs and access to a virtual machine that runs CloseCall. The resulting data specify the spatial organization of RNAs and builds hypotheses for potential regulatory relationships between RNAs. Measurement(s) | RNA • Proximity | Technology Type(s) | RNA sequencing | Factor Type(s) | biological replicate | Sample Characteristic - Organism | Homo sapiens |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11627397
Collapse
Affiliation(s)
- Steven W Wingett
- Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK. .,Bioinformatics, Babraham Institute, Cambridge, UK.
| | | | - Peter Fraser
- Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK.,Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Jörg Morf
- Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK.
| |
Collapse
|
44
|
McDonel P, Guttman M. Approaches for Understanding the Mechanisms of Long Noncoding RNA Regulation of Gene Expression. Cold Spring Harb Perspect Biol 2019; 11:11/12/a032151. [PMID: 31791999 DOI: 10.1101/cshperspect.a032151] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mammalian genomes encode tens of thousands of long noncoding RNAs (lncRNAs) that have been implicated in a diverse array of biological processes and human diseases. In recent years, the development of new tools for studying lncRNAs has enabled important progress in defining the mechanisms by which Xist and other lncRNAs function. This collective work provides a framework for how to define the mechanisms by which lncRNAs act. This includes defining lncRNA function, identifying and characterizing lncRNA-protein interactions, and lncRNA localization in the cell. In this review, we discuss various experimental approaches for deciphering lncRNA mechanisms and discuss issues and limitations in interpreting these results. We explore what these data can reveal about lncRNA function and mechanism as well as emerging insights into lncRNA biology that have been derived from these studies.
Collapse
Affiliation(s)
- Patrick McDonel
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| |
Collapse
|
45
|
Pal K, Forcato M, Jost D, Sexton T, Vaillant C, Salviato E, Mazza EMC, Lugli E, Cavalli G, Ferrari F. Global chromatin conformation differences in the Drosophila dosage compensated chromosome X. Nat Commun 2019; 10:5355. [PMID: 31767860 PMCID: PMC6877619 DOI: 10.1038/s41467-019-13350-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/01/2019] [Indexed: 01/08/2023] Open
Abstract
In Drosophila melanogaster the single male chromosome X undergoes an average twofold transcriptional upregulation for balancing the transcriptional output between sexes. Previous literature hypothesised that a global change in chromosome structure may accompany this process. However, recent studies based on Hi-C failed to detect these differences. Here we show that global conformational differences are specifically present in the male chromosome X and detectable using Hi-C data on sex-sorted embryos, as well as male and female cell lines, by leveraging custom data analysis solutions. We find the male chromosome X has more mid-/long-range interactions. We also identify differences at structural domain boundaries containing BEAF-32 in conjunction with CP190 or Chromator. Weakening of these domain boundaries in male chromosome X co-localizes with the binding of the dosage compensation complex and its co-factor CLAMP, reported to enhance chromatin accessibility. Together, our data strongly indicate that chromosome X dosage compensation affects global chromosome structure.
Collapse
Affiliation(s)
- Koustav Pal
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125, Modena, Italy
| | - Daniel Jost
- University of Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Grenoble, France
- Laboratory of Biology and Modelling of the Cell, University of Lyon, ENS de Lyon, University of Claude Bernard, CNRS UMR 5239, Inserm U1210, F-69007, Lyon, France
| | - Thomas Sexton
- IGH, Institute of Human Genetics, CNRS UPR1142, 141 rue de la Cardonille, 34090, Montpellier, France
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch, France
| | - Cédric Vaillant
- University of Lyon, ENS de Lyon, University of Claude Bernard, CNRS, Laboratoire de Physique, 46 allée d'Italie, 69007, Lyon, France
| | - Elisa Salviato
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Emilia Maria Cristina Mazza
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, Via A. Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, Via A. Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Giacomo Cavalli
- IGH, Institute of Human Genetics, CNRS UPR1142, 141 rue de la Cardonille, 34090, Montpellier, France
| | - Francesco Ferrari
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy.
- Institute of Molecular Genetics, National Research Council, Via Abbiategrasso 207, 27100, Pavia, Italy.
| |
Collapse
|
46
|
Strom AR, Brangwynne CP. The liquid nucleome - phase transitions in the nucleus at a glance. J Cell Sci 2019; 132:132/22/jcs235093. [PMID: 31754043 DOI: 10.1242/jcs.235093] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cells organize membrane-less internal compartments through a process called liquid-liquid phase separation (LLPS) to create chemically distinct compartments, referred to as condensates, which emerge from interactions among biological macromolecules. These condensates include various cytoplasmic structures such as P-granules and stress granules. However, an even wider array of condensates subcompartmentalize the cell nucleus, forming liquid-like structures that range from nucleoli and Cajal bodies to nuclear speckles and gems. Phase separation provides a biophysical assembly mechanism underlying this non-covalent form of fluid compartmentalization and functionalization. In this Cell Science at a Glance article and the accompanying poster, we term these phase-separated liquids that organize the nucleus the liquid nucleome; we discuss examples of biological phase transitions in the nucleus, how the cell utilizes biophysical aspects of phase separation to form and regulate condensates, and suggest interpretations for the role of phase separation in nuclear organization and function.
Collapse
Affiliation(s)
- Amy R Strom
- Department of Chemical and Biological Engineering, Howard Hughes Medical Institute, Princeton University, Princeton NJ 08544, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Howard Hughes Medical Institute, Princeton University, Princeton NJ 08544, USA
| |
Collapse
|
47
|
Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet 2019; 21:102-117. [DOI: 10.1038/s41576-019-0184-5] [Citation(s) in RCA: 296] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/14/2022]
|
48
|
Bousard A, Raposo AC, Żylicz JJ, Picard C, Pires VB, Qi Y, Gil C, Syx L, Chang HY, Heard E, da Rocha ST. The role of Xist-mediated Polycomb recruitment in the initiation of X-chromosome inactivation. EMBO Rep 2019; 20:e48019. [PMID: 31456285 PMCID: PMC6776897 DOI: 10.15252/embr.201948019] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 12/22/2022] Open
Abstract
Xist RNA has been established as the master regulator of X-chromosome inactivation (XCI) in female eutherian mammals, but its mechanism of action remains unclear. By creating novel Xist-inducible mutants at the endogenous locus in male mouse embryonic stem (ES) cells, we dissect the role of the conserved A-B-C-F repeats in the initiation of XCI. We find that transcriptional silencing can be largely uncoupled from Polycomb repressive complex 1 and complex 2 (PRC1/2) recruitment, which requires B and C repeats. Xist ΔB+C RNA specifically loses interaction with PCGF3/5 subunits of PRC1, while binding of other Xist partners is largely unaffected. However, a slight relaxation of transcriptional silencing in Xist ΔB+C indicates a role for PRC1/2 proteins in early stabilization of gene repression. Distinct modules within the Xist RNA are therefore involved in the convergence of independent chromatin modification and gene repression pathways. In this context, Polycomb recruitment seems to be of moderate relevance in the initiation of silencing.
Collapse
Affiliation(s)
- Aurélie Bousard
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
| | - Ana Cláudia Raposo
- Instituto de Medicina MolecularJoão Lobo AntunesFaculdade de MedicinaUniversidade de LisboaLisboaPortugal
| | - Jan Jakub Żylicz
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Christel Picard
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
| | - Vanessa Borges Pires
- Instituto de Medicina MolecularJoão Lobo AntunesFaculdade de MedicinaUniversidade de LisboaLisboaPortugal
- Instituto de Ciências Biomédicas Abel SalazarUniversidade do PortoPortoPortugal
| | - Yanyan Qi
- Center for Dynamic Personal RegulomesStanford UniversityStanfordCAUSA
| | - Cláudia Gil
- Instituto de Medicina MolecularJoão Lobo AntunesFaculdade de MedicinaUniversidade de LisboaLisboaPortugal
| | - Laurène Syx
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
| | - Howard Y Chang
- Center for Dynamic Personal RegulomesStanford UniversityStanfordCAUSA
- Howard Hughes Medical InstituteStanford UniversityStanfordCAUSA
| | - Edith Heard
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
| | - Simão Teixeira da Rocha
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
- Instituto de Medicina MolecularJoão Lobo AntunesFaculdade de MedicinaUniversidade de LisboaLisboaPortugal
| |
Collapse
|
49
|
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Rep 2019; 23:297-312.e12. [PMID: 29617668 PMCID: PMC5906131 DOI: 10.1016/j.celrep.2018.03.064] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 02/12/2018] [Accepted: 03/15/2018] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, and microRNAs in 5,185 TCGA tumors and 1,019 ENCODE assays. Our predictions included hundreds of candidate onco- and tumor-suppressor lncRNAs (cancer lncRNAs) whose somatic alterations account for the dysregulation of dozens of cancer genes and pathways in each of 14 tumor contexts. To demonstrate proof of concept, we showed that perturbations targeting OIP5-AS1 (an inferred tumor suppressor) and TUG1 and WT1-AS (inferred onco-lncRNAs) dysregulated cancer genes and altered proliferation of breast and gynecologic cancer cells. Our analysis indicates that, although most lncRNAs are dysregulated in a tumor-specific manner, some, including OIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergistically dysregulate cancer pathways in multiple tumor contexts. Hundreds of lncRNAs target cancer genes and pathways in each tumor context lncRNA copy numbers are predictive of target cancer gene dysregulation Most lncRNAs are predicted to be transcriptional or post-transcriptional specialists lncRNAs are predicted to synergistically regulate proliferation pathways in cancer
Collapse
|
50
|
The role of long noncoding RNA in major human disease. Bioorg Chem 2019; 92:103214. [PMID: 31499258 DOI: 10.1016/j.bioorg.2019.103214] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are RNAs whose transcripts are longer than 200nt in length and lack the ability to encode proteins due to lack of specific open reading frames. lncRNAs were once thought to represent transcriptome noise or garbage sequences and a byproduct of RNA polymerase II (Pol II), and thereby ignored by researchers. In fact, lncRNA was involved in a wide variety of physiological and pathological processes in organisms. Comprehensive study of lncRNA does not only provide explanations to the physiological and pathological processes of living organisms, but also gives us new perspectives to the diagnosis, prevention and treatment of some clinical diseases. Therefore, the study of lncRNA is a very broad field of great research value and significance. RESULTS This article reviews the function of lncRNAs and their role in major human diseases. CONCLUSIONS Numerous studies show that lncRNA might serve as a biomarker for diagnosis and prognosis of various diseases. Compared to conventional biomarkers, lncRNA seems to have a higher diagnostic and prognostic values, not only because of their tissue and disease specific expression patterns, but also due to their highly stable physical and chemical properties.
Collapse
|