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The Role of long noncoding rnas in Plants

RUSSIAN JOURNAL OF GENETICS 2025年第1期61卷 1-18页

作者： Pronozin, A. Y. Afonnikov, D. A. Russian Acad Sci Inst Cytol & Genet Fed Res Ctr Siberian Branch Novosibirsk 630090 Russia Russian Acad Sci Inst Cytol & Genet Kurchatov Genom Ctr Siberian Branch Novosibirsk 630090 Russia Novosibirsk Natl Res State Univ Novosibirsk 630090 Russia

long noncoding rnas (lncrnas) are a class of linear or circular RNA molecules longer than 200 nucleotides without open reading frames. Experimental studies have shown the involvement of lncrnas in the regulation of resistance to cold, salt, and heat stress and in fruit, root, and leaf development. However, experimental methods are labor-intensive and costly approaches and cannot yet be used for genome-wide mass studies of lncrnas. For this purpose, bioinformatic approaches that aim at large-scale recognition of lncRNA sequences in genomes and transcriptomes have been applied. However, despite the growing number of studies devoted to the structural and functional analysis of lncrnas, this type of molecule remains poorly understood. This is due to the many factors that need to be considered when identifying lncrnas. The use of pan-genomes and pan-transcriptomes will improve the efficiency of the study and the total number of predicted lncrnas compared to using the genome of a single species representative. This review focuses on describing the molecular and biological functions of lncrnas and experimental and bioinformatic methods of identification, patterns of evolution, and detection and analysis of lncrnas at the scale of pan-genomes and pan-transcriptomes.

关键词： long noncoding rnas micrornas transcription regulation pan-genome

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long noncoding rnas: Novel players in colorectal cancer

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CANCER LETTERS 2015年第1期361卷 13-21页

作者： Han, Dong Wang, Meng Ma, Ning Xu, Ya Jiang, Yuting Gao, Xu Harbin Med Univ Dept Biochem & Mol Biol Harbin Peoples R China Heilongjiang Med Sci Acad Harbin Peoples R China Harbin Med Univ Affiliated Hosp 2 Dept Gen Surg Harbin Peoples R China

Colorectal cancer (CRC) is the most common type of cancer in the world. Despite its commonness, the underlying mechanism of CRC is not completely understood. long noncoding rnas (lncrnas) have received increased attention with the development of whole genome and transcriptome sequencing technologies. Recent findings reveal that lncrnas are implicated in serial steps of cancer development. These Incrnas interact with DNA, RNA, protein molecules and/or their combinations, acting as an essential regulator in chromatin organization, and transcriptional and post-transcriptional regulation. In this review, we highlight recent findings of emerging roles for lncrnas in CRC and discuss rapid translational lncRNA research for clinical application in diagnosis, prognosis and potential treatment. (C) 2015 Elsevier Ireland Ltd. All rights reserved.

关键词： long noncoding rnas Colorectal cancer (CRC) Tumorigenesis Therapeutic targets

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long noncoding rnas: New Players in the Osteogenic Differentiation of Bone Marrow- and Adipose-Derived Mesenchymal Stem Cells

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STEM CELL REVIEWS AND REPORTS 2018年第3期14卷 297-308页

作者： Yang, Qiaolin Jia, Lingfei Li, Xiaobei Guo, Runzhi Huang, Yiping Zheng, Yunfei Li, Weiran Peking Univ Sch & Hosp Stomatol Dept Orthodont 22 Zhongguancun Ave South Beijing 100081 Peoples R China Peking Univ Sch & Hosp Stomatol Cent Lab Beijing 100081 Peoples R China Peking Univ Sch & Hosp Stomatol Dept Oral & Maxillofacial Surg Beijing 100081 Peoples R China

Mesenchymal stem cells (MSCs) are an important population of multipotent stem cells that differentiate into multiple lineages and display great potential in bone regeneration and repair. Although the role of protein-coding genes in the osteogenic differentiation of MSCs has been extensively studied, the functions of noncoding rnas in the osteogenic differentiation of MSCs are unclear. The recent application of next-generation sequencing to MSC transcriptomes has revealed that long noncoding rnas (lncrnas) are associated with the osteogenic differentiation of MSCs. Lncrnas are a class of non-coding transcripts of more than 200 nucleotides in length. noncoding rnas are thought to play a key role in osteoblast differentiation through various regulatory mechanisms including chromatin modification, transcription factor binding, competent endogenous mechanism, and other post-transcriptional mechanisms. Here, we review the roles of lncrnas in the osteogenic differentiation of bone marrow- and adipose-derived stem cells and provide a theoretical foundation for future research.

关键词： long noncoding rnas Mesenchymal stem cells Osteogenic differentiation Epigenetics BMSCs ADSCs

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long noncoding rnas and atherosclerosis

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ATHEROSCLEROSIS 2016年 248卷 51-61页

作者： Zhou, Tian Ding, Jia-wang Wang, Xin-An Zheng, Xia-xia China Three Gorges Univ Coll Clin Med Sci 1 Dept Cardiol Yichang 443000 Hubei Province Peoples R China China Three Gorges Univ Inst Cardiovasc Dis Yichang 443000 Hubei Province Peoples R China

Atherosclerosis is universally recognized as a chronic lipid-induced inflammation of the vessel wall in response to dyslipidemia and haemodynamic stress involving dysfunction and activation of resident vascular cells as well as infiltration of leukocytes. As members of nonprotein-coding rnas, the long noncoding rnas (lncrnas) are implicated in various biological processes. Accumulating evidences suggest that lncrnas regulate the function of vascular wall, activation of macrophages, lipid metabolism and immune response. Here, we review the effects of lncrnas on the progress of atherosclerosis. (C) 2016 Elsevier Ireland Ltd. All rights reserved.

关键词： Atherosclerosis long noncoding rnas Lipid Vascular function Vascular inflammation

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long noncoding rnas as Organizers of Nuclear Architecture

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Science China(Life Sciences) 2016年第3期59卷 236-244页

作者： Lu Cheng Hui Ming Minzhe Zhu Bo Wen Department of Biochemistry and Molecular Biology and Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education &Institutes of Biomedical Sciences Shanghai Medical College Fudan University

In the eukaryotic cell nucleus, chromatin and its associated macromolecules must be organized into a higher-ordered conformation to function normally. However, mechanisms underlying the organization and dynamics of the nucleus remain unclear. long noncoding rnas(lnc rnas), i.e., transcripts longer than 200 nucleotides with little or no protein-coding capacity, are increasingly recognized as important regulators in diverse biological processes. Recent studies have shown that some lnc rnas are involved in various aspects of genome organization, including the facilitation of chromosomal interactions and establishment of nuclear bodies, suggesting that lnc rnas act as general organizers of the nuclear architecture. Here, we discuss recent advances in this emerging and intriguing field.

关键词： long noncoding rnas chromatin nuclear architecture

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long noncoding rnas in autoimmune diseases

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JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART A 2019年第2期107卷 468-475页

作者： Xu, Fei Jin, Lei Jin, Yueling Nie, Zhiyan Zheng, Hong Shanghai Univ Med & Hlth Sci Dept Microbiol & Immunol Shanghai 201318 Peoples R China Shanghai Univ Med & Hlth Sci Dept Inspect & Quarantine Shanghai 201318 Peoples R China

With the completion of the human genome project and further development of high-throughput genomic technologies, interest in long noncoding rnas (lncrnas), which are defined as non-protein-coding rnas at least 200 nucleotides in length, has strongly increased, and lncrnas have become a major research direction. Increasing evidence demonstrates that lncrnas are closely related to human growth and development and to disease occurrence via various mechanisms. lncrnas also play crucial roles in the differentiation and activation of immune cells, and their relationships with human autoimmune diseases have received increasing attention. The development of biotechnology has led to the gradual discovery of many potential lncRNA functions. In this review, we discuss various lncrnas that have been implicated in different human autoimmune diseases, focusing on their clinical applications as potential biomarkers and therapeutic targets in the pathologies of diverse human autoimmune diseases. (c) 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 468-475, 2019.

关键词： long noncoding rnas autoimmune diseases systemic lupus erythematosus rheumatoid arthritis psoriasis multiple sclerosis

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long noncoding rnas and Their Role in Oncogenesis

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MOLECULAR BIOLOGY 2018年第6期52卷 787-798页

作者： Bure, I. V. Kuznetsova, E. B. Zaletaev, D. V. Sechenov Univ Sechenov Moscow State Med Univ 1 Inst Mol Med Moscow 119146 Russia Res Ctr Med Genet Moscow 115522 Russia

The noncoding part of the human genome, which was previously considered nonfunctional or junk DNA, has been the subject of extensive research this decade. Nevertheless, long noncoding rnas still represent one of the least investigated fields because of their complexity, multiplicity, and diversity. While some long noncoding rnas have been characterized fairly well, the functions of many others remain poorly understood. long noncoding rnas play an essential role in the regulation of gene expression in all tissues and on all developmental stages. They are involved in a number of signaling pathways, and their aberrant functioning can be pathogenic. This review aims to summarize current state-of-the-art structures of these transcripts in this research field, their genomic localization, their functions, and underlying mechanisms. It also focuses on cancer-associated aberrations of long noncoding rnas, as well as on prospects of their application in tumor diagnostics and therapy. Examples of decreasing the levels of oncogenic long noncoding rnas via silencing with short interfering rnas, antisense oligonucleotides, or low molecular-weight inhibitors are also described.

关键词： long noncoding rnas oncogenesis diagnostics regulation

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long noncoding rnas and the regulation of innate immunity and host-virus interactions

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JOURNAL OF LEUKOCYTE BIOLOGY 2019年第1期106卷 83-93页

作者： Basavappa, Megha Cherry, Sara Henao-Mejia, Jorge Univ Penn Dept Pathol & Lab Med Philadelphia PA 19104 USA Univ Penn Dept Microbiol Philadelphia PA 19104 USA Univ Penn Inst Immunol Perelman Sch Med Philadelphia PA 19104 USA Univ Penn Div Transplant Immunol Dept Pathol & Lab Med Childrens Hosp Philadelphia Philadelphia PA 19104 USA

Immune responses are both pathogen and cell type-specific. The innate arm of immunity is characterized by rapid intracellular signaling cascades resulting in the production of hundreds of antimicrobial effectors that protect the host organism. long noncoding rnas have been shown to operate as potent modulators of both RNA and protein function throughout cell biology. Emerging data suggest that this is also true within innate immunity. Lncrnas have been shown to regulate both innate immune cell identity and the transcription of gene expression programs critical for innate immune responses. Here, we review the diverse roles of lncrnas within innate defense with a specific emphasis on host-virus interactions.

关键词： Innate immunity host-virus interactions long noncoding rnas gene regulation

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long noncoding rnas implicated in embryonic development in Ybx1 knockout zebrafish

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FEBS OPEN BIO 2021年第4期11卷 1259-1276页

作者： Huang, Chen Zhu, Bo Leng, Dongliang Ge, Wei Zhang, Xiaohua Douglas Macau Univ Sci & Technol Macau Inst Appl Res Med & Hlth State Key Lab Qual Res Chinese Med Macau Peoples R China Univ Macau Fac Hlth Sci Taipa Macao Peoples R China

Y-box-binding protein 1 (Ybx1, YB-1), also known as Y-box transcription factor, is involved in a variety of biological processes (BPs) and pathways, including embryogenesis, reproduction and development in vertebrates. Several noncoding rnas regulate Ybx1 signaling. However, the role of long noncoding rnas (lncrnas) in embryogenesis remains incompletely understood. Here, we investigated the possible involvement of lncrnas in Ybx1-mediated regulation of vertebrate development by performing systematic transcriptome analysis of RNA sequencing data derived from ybx1 homozygous mutant zebrafish on day 5 (day5_ybx1(-/-)) and wild-type zebrafish on days 5 and 6 (day5_ybx1(+/+) and day6_ybx1(+/+)). We identified several lncrnas affected by ybx1 disruption that may target reduction-oxidation-related genes, such as duox (NADPH oxidase) and noxo1a (NADPH oxidase organizer). Knockdown of three selected lncrnas led to morphological deformation of larvae, implying an involvement of these lncrnas in zebrafish embryo development. In summary, our study provides new insights into the lncRNA-mediated mechanisms underlying development in Ybx1-deficient zebrafish larvae.

关键词： deep RNA sequencing long noncoding rnas REDOX YBX1 zebrafish embryo development

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long noncoding rnas, Chromatin, and Development

THESCIENTIFICWORLDJOURNAL

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THESCIENTIFICWORLDJOURNAL 2010年第1期10卷 90-102页

作者： Caley, Daniel P. Pink, Ryan C. Trujillano, Daniel Carter, David R. F. Oxford Brookes Univ Sch Life Sci Oxford OX3 0BP England Cranfield Univ Cranfield MK43 0AL Beds England Ctr Genom Regulat CRG UPF Genes & Dis Program Genet Causes Dis Grp Barcelona Spain

The way in which the genome of a multicellular organism can orchestrate the differentiation of trillions of cells and many organs, all from a single fertilized egg, is the subject of intense study. Different cell types can be defined by the networks of genes they express. This differential expression is regulated at the epigenetic level by chromatin modifications, such as DNA and histone methylation, which interact with structural and enzymatic proteins, resulting in the activation or silencing of any given gene. While detailed mechanisms are emerging on the role of different chromatin modifications and how these functions are effected at the molecular level, it is still unclear how their deposition across the epigenomic landscape is regulated in different cells. A raft of recent evidence is accumulating that implicates long noncoding rnas (lncrnas) in these processes. Most genomes studied to date undergo widespread transcription, the majority of which is not translated into proteins. In this review, we will describe recent work suggesting that lncrnas are more than transcriptional "noise", but instead play a functional role by acting as tethers and guides to bind proteins responsible for modifying chromatin and mediating their deposition at specific genomic locations. We suggest that lncrnas are at the heart of developmental regulation, determining the epigenetic status and transcriptional network in any given cell type, and that they provide a means to integrate external differentiation cues with dynamic nuclear responses through the regulation of a metastable epigenome. Better characterization of the lncRNA-protein "interactome" may eventually lead to a new molecular toolkit, allowing researchers and clinicians to modulate the genome at the epigenetic level to treat conditions such as cancer.

关键词： long noncoding rnas lncrnas lincrnas noncoding rnas ncrnas chromatin development transcription epigenetics intergenic transcription epigenomics

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