1
|
Chi P, Wang X, Li J, Yang H, Li K, Zhang Y, Lin S, Yu L, Liu S, Chen L, Ren R, Wu J, Huang Z, Geng J, Deng D. Molecular insights into the inhibition of proton-activated chloride channel by transfer RNA. Cell Res 2024:10.1038/s41422-024-00993-6. [PMID: 38942816 DOI: 10.1038/s41422-024-00993-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 06/16/2024] [Indexed: 06/30/2024] Open
Affiliation(s)
- Pengliang Chi
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiang Wang
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jialu Li
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Kaiju Li
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Yuqi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Westlake Laboratory of Life Sciences and Biomedicine, Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Shiyi Lin
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Westlake Laboratory of Life Sciences and Biomedicine, Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Leiye Yu
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, the Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Shiqi Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Lu Chen
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ruobing Ren
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, the Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Jianping Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Westlake Laboratory of Life Sciences and Biomedicine, Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Zhuo Huang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
| | - Jia Geng
- Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China.
| | - Dong Deng
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, China.
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, Sichuan, China.
| |
Collapse
|
2
|
Oliveira JIN, Cabral-de-Mello DC, Valente GT, Martins C. Transcribing the enigma: the B chromosome as a territory of uncharted RNAs. Genetics 2024; 227:iyae026. [PMID: 38513121 DOI: 10.1093/genetics/iyae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/10/2024] [Indexed: 03/23/2024] Open
Abstract
B chromosomes are supernumerary elements found in several groups of eukaryotes, including fungi, plants, and animals. Typically, these chromosomes either originate from their hosts through errors in meiosis or interspecifically through horizontal transfer. While many B chromosomes are primarily heterochromatic and possess a low number of coding genes, these additional elements are still capable of transcribing sequences and exerting influence on the expression of host genes. How B chromosomes escape elimination and which impacts can be promoted in the cell always intrigued the cytogeneticists. In pursuit of understanding the behavior and functional impacts of these extra elements, cytogenetic studies meet the advances of molecular biology, incorporating various techniques into investigating B chromosomes from a functional perspective. In this review, we present a timeline of studies investigating B chromosomes and RNAs, highlighting the advances and key findings throughout their history. Additionally, we identified which RNA classes are reported in the B chromosomes and emphasized the necessity for further investigation into new perspectives on the B chromosome functions. In this context, we present a phylogenetic tree that illustrates which branches either report B chromosome presence or have functional RNA studies related to B chromosomes. We propose investigating other unexplored RNA classes and conducting functional analysis in conjunction with cytogenetic studies to enhance our understanding of the B chromosome from an RNA perspective.
Collapse
Affiliation(s)
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro 13506-900, Brazil
| | - Guilherme T Valente
- Applied Biotechnology Laboratory, Clinical Hospital of Botucatu Medical School, Botucatu 18618-687, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu 18618-689, Brazil
| |
Collapse
|
3
|
Abasi M, Ranjbari J, Ghanbarian H. 7SK small nuclear RNA (Rn7SK) induces apoptosis through intrinsic and extrinsic pathways in human embryonic kidney cell line. Mol Biol Rep 2024; 51:96. [PMID: 38193993 DOI: 10.1007/s11033-023-08934-z] [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: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Rn7SK, a highly conserved small nuclear non-coding RNA, controls Polymerase II transcription machinery by activating of the Positive Transcriptional Elongation Factor b (P-TEFb). Apart from its role in transcriptional regulation, the potential functions of Rn7SK in cell apoptosis are poorly understood. In a previous study, we demonstrated that overexpression of 7SK induces apoptosis in HEK cells. However, it remains unclear whether 7SK-mediated apoptosis induction is exerted through the intrinsic or extrinsic pathways. METHODS AND RESULTS Rn7SK was overexpressed in HEK 293T cell line using Lipofectamine 2000 reagent to investigate its potential apoptotic functions. The overexpression of Rn7SK resulted in reduced cell viability through the induction of apoptosis, as evidenced by MTT assay and Annexin V/PI staining. Concurrently, alterations in the expression levels of key apoptosis-related genes were observed, as determined by quantitative RT-PCR. Furthermore, Rn7SK overexpression led to a decrease in cell proliferation, as assessed by colony formation assay and growth curve analysis. This reduction was associated with downregulated expression of key proliferative-related genes. Additionally, the migration and invasion capabilities of cells were significantly inhibited upon upregulation of Rn7SK, as demonstrated by transwell assays. CONCLUSIONS This study suggests the apoptotic role of 7SK through both intrinsic and extrinsic pathways, necessitating further investigation into its underlying mechanisms.
Collapse
Affiliation(s)
- Mozhgan Abasi
- Immunogenetics Research Center, Department of Tissue Engineering and Applied Cell Sciences, Faculty of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Molecular and Cell Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Javad Ranjbari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Ghanbarian
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
4
|
Fafard-Couture É, Labialle S, Scott MS. The regulatory roles of small nucleolar RNAs within their host locus. RNA Biol 2024; 21:1-11. [PMID: 38626213 PMCID: PMC11028025 DOI: 10.1080/15476286.2024.2342685] [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] [Accepted: 04/08/2024] [Indexed: 04/18/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) are a class of conserved noncoding RNAs forming complexes with proteins to catalyse site-specific modifications on ribosomal RNA. Besides this canonical role, several snoRNAs are now known to regulate diverse levels of gene expression. While these functions are carried out in trans by mature snoRNAs, evidence has also been emerging of regulatory roles of snoRNAs in cis, either within their genomic locus or as longer transcription intermediates during their maturation. Herein, we review recent findings that snoRNAs can interact in cis with their intron to regulate the expression of their host gene. We also explore the ever-growing diversity of longer host-derived snoRNA extensions and their functional impact across the transcriptome. Finally, we discuss the role of snoRNA duplications into forging these new layers of snoRNA-mediated regulation, as well as their involvement in the genomic imprinting of their host locus.
Collapse
Affiliation(s)
- Étienne Fafard-Couture
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Michelle S Scott
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| |
Collapse
|
5
|
Bian Z, Xu C, Xie Y, Wang X, Chen Y, Mao S, Wu Q, Zhu J, Huang N, Zhang Y, Ma J, Sun F, Pan Q. SNORD11B-mediated 2'-O-methylation of primary let-7a in colorectal carcinogenesis. Oncogene 2023; 42:3035-3046. [PMID: 37620450 DOI: 10.1038/s41388-023-02808-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/27/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Evidence indicates that small nucleolar RNAs (snoRNAs) participate in tumorigenesis and development and could be promising biomarkers for colorectal cancer (CRC). Here, we examine the profile of snoRNAs in CRC and find that expression of SNORD11B is increased in CRC tumor tissues and cell lines, with a significant positive correlation between SNORD11B expression and that of its host gene NOP58. SNORD11B promotes CRC cell proliferation and invasion and inhibits apoptosis. Mechanistically, SNORD11B promotes the processing and maturation of 18 S ribosomal RNA (rRNA) by mediating 2'-O-methylated (Nm) modification on the G509 site of 18 S rRNA. Intriguingly, SNORD11B mediates Nm modification on the G225 site of MIRLET7A1HG (pri-let-7a) with a canonical motif, resulting in degradation of pri-let-7a, inhibition of DGCR8 binding, reduction in mature tumor suppressor gene let-7a-5p expression, and upregulation of downstream oncogene translation. SNORD11B performs comparably to CEA and CA199 in diagnosing CRC. High expression of SNORD11B is significantly correlated with a more advanced TNM stage and lymph node metastasis, which indicates poor prognosis.
Collapse
Affiliation(s)
- Zhixuan Bian
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China
- Department of Laboratory Medicine, Sanya Women and Children's Hospital Managed by Shanghai Children's Medical Center, Sanya, 572000, China
| | - Chang Xu
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Yi Xie
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China
| | - Xiaoying Wang
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Yan Chen
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Siwei Mao
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China
| | - Qi Wu
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Jiabei Zhu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China
| | - Nan Huang
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Yue Zhang
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China
| | - Ji Ma
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China
| | - Fenyong Sun
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, China.
| | - Qiuhui Pan
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, China.
- Department of Laboratory Medicine, Sanya Women and Children's Hospital Managed by Shanghai Children's Medical Center, Sanya, 572000, China.
| |
Collapse
|
6
|
Guo D, Yang M, Li S, Zhu W, Chen M, Pan J, Long D, Liu Z, Zhang C. Expression and molecular regulation of non-coding RNAs in HPV-positive head and neck squamous cell carcinoma. Front Oncol 2023; 13:1122982. [PMID: 37064141 PMCID: PMC10090466 DOI: 10.3389/fonc.2023.1122982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/06/2023] [Indexed: 03/31/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent malignancy worldwide. Accumulating evidence suggests that persistent HPV infection is closely related to a subset of HNSCC types, and the incidence of human papillomavirus (HPV)-positive HNSCC has been annually increasing in recent decades. Although the carcinogenesis of HPV-positive HNSCC has not been completely elucidated, it has been well confirmed that E6 and E7, the main viral oncoproteins are responsible for the maintenance of malignant transformation, promotion of cell proliferation, and increase in tumor invasion. Moreover, compared with HPV-negative HNSCC, HPV-positive HNSCC shows some special clinical-pathological features, which are possibly related to HPV infection and their specific regulatory mechanisms. Non-coding RNA (ncRNA) is a class of RNA lacking the protein-coding function and playing a critical regulatory role via multiple complex molecular mechanisms. NcRNA is an important regulatory pattern of epigenetic modification, which can exert significant effects on HPV-induced tumorigenesis and progression by deregulating downstream genes. However, the knowledge of ncRNAs is still limited, hence, a better understanding of ncRNAs could provide some insights for exploring the carcinogenesis mechanism and identifying valuable biomarkers in HPV-positive HNSCC. Therefore, in this review, we mainly focused on the expression profile of ncRNAs (including lncRNA, miRNA, and circRNA) and explored their regulatory role in HPV-positive HNSCC, aiming to clarify the regulatory mechanism of ncRNAs and identify valuable biomarkers for HPV-positive HNSCC.
Collapse
|
7
|
Emami Meybodi SM, Soleimani N, Yari A, Javadifar A, Tollabi M, Karimi B, Emami Meybodi M, Seyedhossaini S, Brouki Milan P, Dehghani Firoozabadi A. Circulatory long noncoding RNAs (circulatory-LNC-RNAs) as novel biomarkers and therapeutic targets in cardiovascular diseases: Implications for cardiovascular diseases complications. Int J Biol Macromol 2023; 225:1049-1071. [PMID: 36414082 DOI: 10.1016/j.ijbiomac.2022.11.167] [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: 09/28/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022]
Abstract
Cardiovascular diseases (CVDs) are a group of disorders with major global health consequences. The prevalence of CVDs continues to grow due to population-aging and lifestyle modifications. Non-coding RNAs (ncRNAs) as key regulators of cell signaling pathways have gained attention in the occurrence and development of CVDs. Exosomal-lncRNAs (exos-lncRNAs) are emerging biomarkers due to their high sensitivity and specificity, stability, accuracy and accessibility in the biological fluids. Recently, circulatory and exos-based-lncRNAs are emerging and novel bio-tools in various pathogenic conditions. It is worth mentioning that dysregulation of these molecules has been found in different types of CVDs. In this regard, we aimed to discuss the knowledge gaps and suggest research priorities regarding circulatory and exos-lncRNAs as novel bio-tools and therapeutic targets for CVDs.
Collapse
Affiliation(s)
- Seyed Mahdi Emami Meybodi
- Yazd Cardiovascular Research Center, Non-communicable Diseases Research Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Nafiseh Soleimani
- Yazd Cardiovascular Research Center, Non-communicable Diseases Research Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Abolfazl Yari
- Cellular and Molecular Research Center, Birjand University of Medical Mciences, Birjand, Iran.
| | - Amin Javadifar
- Immunology Research Center, Inflammation and Inflammatory Disease Division, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Tollabi
- Department of Tissue Engineering & Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Bahareh Karimi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mahmoud Emami Meybodi
- Yazd Cardiovascular Research Center, Non-communicable Diseases Research Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Seyedmostafa Seyedhossaini
- Yazd Cardiovascular Research Center, Non-communicable Diseases Research Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Peiman Brouki Milan
- Department of Tissue Engineering & Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Ali Dehghani Firoozabadi
- Department of Tissue Engineering & Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
8
|
Huo C, Zhang B, Wang R. Research progress on plant noncoding RNAs in response to low-temperature stress. PLANT SIGNALING & BEHAVIOR 2022; 17:2004035. [PMID: 34927551 PMCID: PMC8932918 DOI: 10.1080/15592324.2021.2004035] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Low temperature (LT) is an important factor limiting plant growth and distribution. Plants have evolved sophisticated adaptive mechanisms to cope with hypothermia. RNA silencing is the orchestrator of these cellular responses. RNA silencing, which modifies gene expression through noncoding RNAs (ncRNAs), is a strategy used by plants to combat environmental stress. ncRNAs, which have very little protein-coding capacity, work by binding reverse complementary endogenous transcripts. In plants, ncRNAs include small non-coding RNAs (sncRNAs), medium-sized non-coding RNAs (mncRNAs), and long non-coding RNAs (lncRNAs). Apart from describing the biogenesis of different ncRNAs (miRNAs, siRNAs, and lncRNAs), we thoroughly discuss the functions of these ncRNAs during cold acclimation. Two major classes of sncRNAs, microRNAs and siRNAs, play essential regulatory roles in cold response processes through the posttranscriptional gene silencing (PTGS) pathway or transcriptional gene silencing (TGS) pathway. Microarray or transcriptome sequencing analysis can reveal a large number of cold-responsive miRNAs in plants. In this review, the cold-response patterns of miRNAs verified by Northern blotting or quantitative PCR in Arabidopsis thaliana, rice, and many other important crops are discussed. The detailed molecular mechanisms of several miRNAs in Arabidopsis (miR397, miR408, miR402, and miR394) and rice (Osa-miR156, Osa-miR319, and Osa-miR528) that regulate plant cold resistance are elucidated. In addition, the regulatory mechanism of the lncRNA SVALKA in the cold signaling pathway is explained in detail. Finally, we present the challenges for understanding the roles of small ncRNAs in cold signal transduction.
Collapse
Affiliation(s)
- Chenmin Huo
- College of Biology Science & Engineering, Hebei University of Economics & Business, Shijiazhuang, China
| | - Baowen Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ruiju Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- CONTACT Ruiju Wang College of Biology Science & Engineering, Hebei University of Economics & Business, Shijiazhuang, China
| |
Collapse
|
9
|
Midsize noncoding RNAs in cancers: a new division that clarifies the world of noncoding RNA or an unnecessary chaos? Rep Pract Oncol Radiother 2022; 27:1077-1093. [PMID: 36632289 PMCID: PMC9826665 DOI: 10.5603/rpor.a2022.0123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/18/2022] [Indexed: 12/31/2022] Open
Abstract
Most of the human genome is made out of noncoding RNAs (ncRNAs). These ncRNAs do not code for proteins but carry a vast number of important functions in human cells such as: modification and processing other RNAs (tRNAs, rRNAs, snRNAs, snoRNAs, miRNAs), help in the synthesis of ribosome proteins, initiation of DNA replication, regulation of transcription, processing of pre-messenger mRNA during its maturation and much more. The ncRNAs also have a significant impact on many events that occur during carcinogenesis in cancer cells, such as: regulation of cell survival, cellular signaling, apoptosis, proliferation or even influencing the metastasis process. The ncRNAs may be divided based on their length, into short and long, where 200 nucleotides is the "magic" border. However, a new division was proposed, suggesting the creation of the additional group called midsize noncoding RNAs, with the length ranging from 50-400 nucleotides. This new group may include: transfer RNA (tRNA), small nuclear RNAs (snRNAs) with 7SK and 7SL, small nucleolar RNAs (snoRNAs), small Cajal body-specific RNAs (scaRNAs) and YRNAs. In this review their structure, biogenesis, function and influence on carcinogenesis process will be evaluated. What is more, a question will be answered of whether this new division is a necessity that clears current knowledge or just creates an additional misunderstanding in the ncRNA world?
Collapse
|
10
|
Nazzari M, Hauser D, van Herwijnen M, Romitti M, Carvalho DJ, Kip AM, Caiment F. CODA: a combo-Seq data analysis workflow. Brief Bioinform 2022; 24:6955042. [PMID: 36545800 PMCID: PMC9851309 DOI: 10.1093/bib/bbac582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
The analysis of the combined mRNA and miRNA content of a biological sample can be of interest for answering several research questions, like biomarkers discovery, or mRNA-miRNA interactions. However, the process is costly and time-consuming, separate libraries need to be prepared and sequenced on different flowcells. Combo-Seq is a library prep kit that allows us to prepare combined mRNA-miRNA libraries starting from very low total RNA. To date, no dedicated bioinformatics method exists for the processing of Combo-Seq data. In this paper, we describe CODA (Combo-seq Data Analysis), a workflow specifically developed for the processing of Combo-Seq data that employs existing free-to-use tools. We compare CODA with exceRpt, the pipeline suggested by the kit manufacturer for this purpose. We also evaluate how Combo-Seq libraries analysed with CODA perform compared with conventional poly(A) and small RNA libraries prepared from the same samples. We show that using CODA more successfully trimmed reads are recovered compared with exceRpt, and the difference is more dramatic with short sequencing reads. We demonstrate how Combo-Seq identifies as many genes and fewer miRNAs compared to the standard libraries, and how miRNA validation favours conventional small RNA libraries over Combo-Seq. The CODA code is available at https://github.com/marta-nazzari/CODA.
Collapse
Affiliation(s)
- Marta Nazzari
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Duncan Hauser
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Marcel van Herwijnen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Mírian Romitti
- Institute of Interdisciplinary Research in Molecular Human Biology (IRIBHM), Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Daniel J Carvalho
- Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Anna M Kip
- Department of Complex Tissue Regeneration, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Florian Caiment
- Corresponding author: Florian Caiment, Tel.: +31433881218; E-mail:
| |
Collapse
|
11
|
Marchetti L, Nifosì R, Martelli PL, Da Pozzo E, Cappello V, Banterle F, Trincavelli ML, Martini C, D’Elia M. Quantum computing algorithms: getting closer to critical problems in computational biology. Brief Bioinform 2022; 23:6758194. [PMID: 36220772 PMCID: PMC9677474 DOI: 10.1093/bib/bbac437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022] Open
Abstract
The recent biotechnological progress has allowed life scientists and physicians to access an unprecedented, massive amount of data at all levels (molecular, supramolecular, cellular and so on) of biological complexity. So far, mostly classical computational efforts have been dedicated to the simulation, prediction or de novo design of biomolecules, in order to improve the understanding of their function or to develop novel therapeutics. At a higher level of complexity, the progress of omics disciplines (genomics, transcriptomics, proteomics and metabolomics) has prompted researchers to develop informatics means to describe and annotate new biomolecules identified with a resolution down to the single cell, but also with a high-throughput speed. Machine learning approaches have been implemented to both the modelling studies and the handling of biomedical data. Quantum computing (QC) approaches hold the promise to resolve, speed up or refine the analysis of a wide range of these computational problems. Here, we review and comment on recently developed QC algorithms for biocomputing, with a particular focus on multi-scale modelling and genomic analyses. Indeed, differently from other computational approaches such as protein structure prediction, these problems have been shown to be adequately mapped onto quantum architectures, the main limit for their immediate use being the number of qubits and decoherence effects in the available quantum machines. Possible advantages over the classical counterparts are highlighted, along with a description of some hybrid classical/quantum approaches, which could be the closest to be realistically applied in biocomputation.
Collapse
Affiliation(s)
| | | | - Pier Luigi Martelli
- Corresponding authors: Pier Luigi Martelli. Tel.: +39 0512094005; Fax: +39 0512094005; E-mail: ; Claudia Martini. Tel.: +39 0502219522; Fax: +39 050 2210680; E-mail:
| | - Eleonora Da Pozzo
- University of Pisa, Department of Pharmacy, via Bonanno 6, 56126 Pisa Italy
| | - Valentina Cappello
- Italian Institute of Technology, Center for Materials Interfaces, Viale Rinaldo Piaggio 34, 56025 Pontedera (PI), Italy
| | | | | | - Claudia Martini
- Corresponding authors: Pier Luigi Martelli. Tel.: +39 0512094005; Fax: +39 0512094005; E-mail: ; Claudia Martini. Tel.: +39 0502219522; Fax: +39 050 2210680; E-mail:
| | - Massimo D’Elia
- University of Pisa, Department of Physics, Largo Bruno Pontecorvo 3, 56127, Pisa Italy
- INFN, Sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| |
Collapse
|
12
|
Diffendall GM, Barcons-Simon A, Baumgarten S, Dingli F, Loew D, Scherf A. Discovery of RUF6 ncRNA-interacting proteins involved in P. falciparum immune evasion. Life Sci Alliance 2022; 6:6/1/e202201577. [PMID: 36379669 PMCID: PMC9670795 DOI: 10.26508/lsa.202201577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are emerging regulators of immune evasion and transmission of Plasmodium falciparum RUF6 is an ncRNA gene family that is transcribed by RNA polymerase III but actively regulates the Pol II-transcribed var virulence gene family. Understanding how RUF6 ncRNA connects to downstream effectors is lacking. We developed an RNA-directed proteomic discovery (ChIRP-MS) protocol to identify in vivo RUF6 ncRNA-protein interactions. The RUF6 ncRNA interactome was purified with biotinylated antisense oligonucleotides. Quantitative label-free mass spectrometry identified several unique proteins linked to gene transcription including RNA Pol II subunits, nucleosome assembly proteins, and a homologue of DEAD box helicase 5 (DDX5). Affinity purification of Pf-DDX5 identified proteins originally found by our RUF6-ChIRP protocol, validating the technique's robustness for identifying ncRNA interactomes in P. falciparum Inducible displacement of nuclear Pf-DDX5 resulted in significant down-regulation of the active var gene. Our work identifies a RUF6 ncRNA-protein complex that interacts with RNA Pol II to sustain the var gene expression, including a helicase that may resolve G-quadruplex secondary structures in var genes to facilitate transcriptional activation and progression.
Collapse
Affiliation(s)
- Gretchen M Diffendall
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France,Sorbonne Université Ecole doctorale Complexité du Vivant ED515, Paris, France
| | - Anna Barcons-Simon
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France,Sorbonne Université Ecole doctorale Complexité du Vivant ED515, Paris, France,Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Artur Scherf
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France
| |
Collapse
|
13
|
Current Status of Regulatory Non-Coding RNAs Research in the Tritryp. Noncoding RNA 2022; 8:ncrna8040054. [PMID: 35893237 PMCID: PMC9326685 DOI: 10.3390/ncrna8040054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022] Open
Abstract
Trypanosomatids are protozoan parasites that cause devastating vector-borne human diseases. Gene expression regulation of these organisms depends on post-transcriptional control in responding to diverse environments while going through multiple developmental stages of their complex life cycles. In this scenario, non-coding RNAs (ncRNAs) are excellent candidates for a very efficient, quick, and economic strategy to regulate gene expression. The advent of high throughput RNA sequencing technologies show the presence and deregulation of small RNA fragments derived from canonical ncRNAs. This review seeks to depict the ncRNA landscape in trypanosomatids, focusing on the small RNA fragments derived from functional RNA molecules observed in RNA sequencing studies. Small RNA fragments derived from canonical ncRNAs (tsRNAs, snsRNAs, sdRNAs, and sdrRNAs) were identified in trypanosomatids. Some of these RNAs display changes in their levels associated with different environments and developmental stages, demanding further studies to determine their functional characterization and potential roles. Nevertheless, a comprehensive and detailed ncRNA annotation for most trypanosomatid genomes is still needed, allowing better and more extensive comparative and functional studies.
Collapse
|
14
|
Chen TY, Gonzalez-Kozlova E, Soleymani T, La Salvia S, Kyprianou N, Sahoo S, Tewari AK, Cordon-Cardo C, Stolovitzky G, Dogra N. Extracellular vesicles carry distinct proteo-transcriptomic signatures that are different from their cancer cell of origin. iScience 2022; 25:104414. [PMID: 35663013 PMCID: PMC9157216 DOI: 10.1016/j.isci.2022.104414] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/22/2021] [Accepted: 05/12/2022] [Indexed: 12/11/2022] Open
Abstract
Circulating extracellular vesicles (EVs) contain molecular footprints-lipids, proteins, RNA, and DNA-from their cell of origin. Consequently, EV-associated RNA and proteins have gained widespread interest as liquid-biopsy biomarkers. Yet, an integrative proteo-transcriptomic landscape of EVs and comparison with their cell of origin remains obscure. Here, we report that EVs enrich distinct proteo-transcriptome that does not linearly correlate with their cell of origin. We show that EVs enrich endosomal and extracellular proteins, small RNA (∼13-200 nucleotides) associated with cell differentiation, development, and Wnt signaling. EVs cargo specific RNAs (RNY3, vtRNA, and MIRLET-7) and their complementary proteins (YBX1, IGF2BP2, and SRSF1/2). To ensure an unbiased and independent analyses, we studied 12 cancer cell lines, matching EVs (inhouse and exRNA database), and serum EVs of patients with prostate cancer. Together, we show that EV-RNA-protein complexes may constitute a functional interaction network to protect and regulate molecular access until a function is achieved.
Collapse
Affiliation(s)
- Tzu-Yi Chen
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Edgar Gonzalez-Kozlova
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Taliah Soleymani
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Sabrina La Salvia
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Natasha Kyprianou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Susmita Sahoo
- Department of Cardiology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Ashutosh K. Tewari
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gustavo Stolovitzky
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
- Sema4, Stamford, CT 06902, USA
| | - Navneet Dogra
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
| |
Collapse
|
15
|
Deschamps-Francoeur G, Couture S, Abou-Elela S, Scott MS. The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets. Nucleic Acids Res 2022; 50:6067-6083. [PMID: 35657102 PMCID: PMC9226514 DOI: 10.1093/nar/gkac475] [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: 11/22/2021] [Revised: 04/13/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Box C/D small nucleolar RNAs (snoRNAs) are a conserved class of RNA known for their role in guiding ribosomal RNA 2'-O-ribose methylation. Recently, C/D snoRNAs were also implicated in regulating the expression of non-ribosomal genes through different modes of binding. Large scale RNA-RNA interaction datasets detect many snoRNAs binding messenger RNA, but are limited by specific experimental conditions. To enable a more comprehensive study of C/D snoRNA interactions, we created snoGloBe, a human C/D snoRNA interaction predictor based on a gradient boosting classifier. SnoGloBe considers the target type, position and sequence of the interactions, enabling it to outperform existing predictors. Interestingly, for specific snoRNAs, snoGloBe identifies strong enrichment of interactions near gene expression regulatory elements including splice sites. Abundance and splicing of predicted targets were altered upon the knockdown of their associated snoRNA. Strikingly, the predicted snoRNA interactions often overlap with the binding sites of functionally related RNA binding proteins, reinforcing their role in gene expression regulation. SnoGloBe is also an excellent tool for discovering viral RNA targets, as shown by its capacity to identify snoRNAs targeting the heavily methylated SARS-CoV-2 RNA. Overall, snoGloBe is capable of identifying experimentally validated binding sites and predicting novel sites with shared regulatory function.
Collapse
Affiliation(s)
- Gabrielle Deschamps-Francoeur
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sonia Couture
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou-Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| |
Collapse
|
16
|
The tRNA-Derived Fragment tRF-24-V29K9UV3IU Functions as a miRNA-like RNA to Prevent Gastric Cancer Progression by Inhibiting GPR78 Expression. JOURNAL OF ONCOLOGY 2022; 2022:8777697. [PMID: 35535309 PMCID: PMC9077451 DOI: 10.1155/2022/8777697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/10/2022] [Indexed: 02/05/2023]
Abstract
Emerging studies have proved that tRNA-derived fragments (tRFs) play vital roles in tumor metastasis; however, the function of tRFs in gastric cancer (GC) remains largely unclear. We investigated the role of tRF-24-V29K9UV3IU in growth and metastasis of GC using a xenograft mouse model. Differential gene expression downstream of tRF-24-V29K9UV3IU was identified by transcriptome sequencing, and interaction was then verified by a dual luciferase reporter and RNA immunoprecipitation. MKN-45 cells were also used to explore the biological functions of tRF-24-V29K9UV3IU in vitro. Here, knockdown of tRF-24-V29K9UV3IU promoted tumor growth and metastasis of GC in vivo. The expression of tRF-24-V29K9UV3IU and E-cadherin (epithelial cell marker) was down-regulated in tumors of mice following tRF-24-V29K9UV3IU knockdown, whereas the mesenchymal cell markers N-cadherin and vimentin displayed an opposite trend. Transcriptome sequencing identified 87 differentially expressed genes (DEGs) down-regulated in the tRF-24-V29K9UV3IU-overexpressed groups compared with the control group. Among them, G-protein–coupled receptor 78 (GPR78), the most significantly down-regulated DEG, was also predicted to be a target of tRF-24-V29K9UV3IU. Moreover, tRF-24-V29K9UV3IU could function as a miRNA-like fragment and bind to AGO2 and directly silence GPR78 expression by complementing with the 3′-untranslated region of the GPR78 mRNA. Functionally, overexpression of tRF-24-V29K9UV3IU significantly suppressed proliferation, migration, and invasion and promoted apoptosis of MKN-45 cells, whereas GPR78 attenuated these effects. Therefore, our data suggest that tRF-24-V29K9UV3IU functions as a miRNA-like fragment to suppress GPR78 expression and thus inhibit GC progression. These observations suggest that the tRF-24-V29K9UV3IU/GPR78 axis serves as a potential therapeutic target in GC.
Collapse
|
17
|
Donda K, Torres BA, Maheshwari A. Non-coding RNAs in Neonatal Necrotizing Enterocolitis. NEWBORN 2022; 1:120-130. [PMID: 35754997 PMCID: PMC9219563 DOI: 10.5005/jp-journals-11002-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Keyur Donda
- Department of Pediatrics, University of South Florida Health Morsani College of Medicine, Tampa, Florida, United States of America
| | - Benjamin A Torres
- Department of Pediatrics, University of South Florida Health Morsani College of Medicine, Tampa, Florida, United States of America
| | - Akhil Maheshwari
- Global Newborn Society, Clarksville, Maryland, United States of America
| |
Collapse
|
18
|
Salehi S, Afzali S, Shahi A, Amirzargar AA, Mansoori Y. Potential Roles of Long Noncoding RNAs as Therapeutic Targets in Organ Transplantation. Front Immunol 2022; 13:835746. [PMID: 35359941 PMCID: PMC8962195 DOI: 10.3389/fimmu.2022.835746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Organ transplantation is the most preferred treatment option for end-stage organ diseases; however, allograft rejection is the major hurdle in successful long-term transplant survival. In spite of developing better HLA matching and more effective immunosuppressive regimen, one-year graft survival has been increased by nearly 90% and the incidence of acute rejection by one-year post-transplantation has been decreased by 12.2% in the last decades, chronic allograft rejection has remained as one of the major obstacles to the long-lasting survival of the transplanted allograft. Therefore, seemingly preventing the allograft rejection and inducing immunological tolerance against transplanted allografts is one of the primary goals in transplantation research to enable long-lasting graft survival. Various mechanisms such as long noncoding RNAs (lncRNAs) have been proposed that induce immune tolerance by modulating the gene expression and regulating innate and adaptive immune responses during transplantation. Besides, because of involvement in regulating epigenetic, transcriptional, and post-translational mechanisms, lncRNAs could affect allograft status. Therefore, these molecules could be considered as the potential targets for prediction, prognosis, diagnosis, and treatment of graft rejection. It is suggested that the noninvasive predictive biomarkers hold promise to overcome the current limitations of conventional tissue biopsy in the diagnosis of rejection. Hence, this review aims to provide a comprehensive overview of lncRNAs and their function to facilitate diagnosis, prognosis, and prediction of the risk of graft rejection, and the suggestive therapeutic choices after transplantation.
Collapse
Affiliation(s)
- Saeedeh Salehi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shima Afzali
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Shahi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Ali Akbar Amirzargar
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yaser Mansoori
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| |
Collapse
|
19
|
Faucher-Giguère L, Roy A, Deschamps-Francoeur G, Couture S, Nottingham RM, Lambowitz AM, Scott MS, Abou Elela S. High-grade ovarian cancer associated H/ACA snoRNAs promote cancer cell proliferation and survival. NAR Cancer 2022; 4:zcab050. [PMID: 35047824 PMCID: PMC8759569 DOI: 10.1093/narcan/zcab050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 01/10/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) are an omnipresent class of non-coding RNAs involved in the modification and processing of ribosomal RNA (rRNA). As snoRNAs are required for ribosome production, the increase of which is a hallmark of cancer development, their expression would be expected to increase in proliferating cancer cells. However, assessing the nature and extent of snoRNAs' contribution to cancer biology has been largely limited by difficulties in detecting highly structured RNA. In this study, we used a dedicated midsize non-coding RNA (mncRNA) sensitive sequencing technique to accurately survey the snoRNA abundance in independently verified high-grade serous ovarian carcinoma (HGSC) and serous borderline tumour (SBT) tissues. The results identified SNORA81, SNORA19 and SNORA56 as an H/ACA snoRNA signature capable of discriminating between independent sets of HGSC, SBT and normal tissues. The expression of the signature SNORA81 correlates with the level of ribosomal RNA (rRNA) modification and its knockdown inhibits 28S rRNA pseudouridylation and accumulation leading to reduced cell proliferation and migration. Together our data indicate that specific subsets of H/ACA snoRNAs may promote tumour aggressiveness by inducing rRNA modification and synthesis.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Sherif Abou Elela
- To whom correspondence should be addressed. Tel: +1 819 821 8000 (Ext 75275);
| |
Collapse
|
20
|
Liu Q. The Emerging Landscape of Long Non-Coding RNAs in Wilms Tumor. Front Oncol 2022; 11:780925. [PMID: 35127486 PMCID: PMC8807488 DOI: 10.3389/fonc.2021.780925] [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: 10/11/2021] [Accepted: 12/29/2021] [Indexed: 11/17/2022] Open
Abstract
Long noncoding RNAs (LncRNAs) are transcripts of nucleic acid sequences with a length of more than 200 bp, which have only partial coding capabilities. Recent studies have shown that lncRNAs located in the nucleus or cytoplasm can be used as gene expression regulatory elements due to their important regulatory effects in a variety of biological processes. Wilms tumor (WT) is a common abdominal tumor in children whose pathogenesis remains unclear. In recent years, many specifically expressed lncRNAs have been found in WT, which affect the occurrence and development of WT. At the same time, lncRNAs may have the capacity to become novel biomarkers for the diagnosis and prognosis of WT. This article reviews related research progress on the relationship between lncRNAs and WT, to provide a new direction for clinical diagnosis and treatment of WT.
Collapse
|
21
|
Hita A, Brocart G, Fernandez A, Rehmsmeier M, Alemany A, Schvartzman S. MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts. BMC Bioinformatics 2022; 23:39. [PMID: 35030988 PMCID: PMC8760670 DOI: 10.1186/s12859-021-04544-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/20/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Total-RNA sequencing (total-RNA-seq) allows the simultaneous study of both the coding and the non-coding transcriptome. Yet, computational pipelines have traditionally focused on particular biotypes, making assumptions that are not fullfilled by total-RNA-seq datasets. Transcripts from distinct RNA biotypes vary in length, biogenesis, and function, can overlap in a genomic region, and may be present in the genome with a high copy number. Consequently, reads from total-RNA-seq libraries may cause ambiguous genomic alignments, demanding for flexible quantification approaches. RESULTS Here we present Multi-Graph count (MGcount), a total-RNA-seq quantification tool combining two strategies for handling ambiguous alignments. First, MGcount assigns reads hierarchically to small-RNA and long-RNA features to account for length disparity when transcripts overlap in the same genomic position. Next, MGcount aggregates RNA products with similar sequences where reads systematically multi-map using a graph-based approach. MGcount outputs a transcriptomic count matrix compatible with RNA-sequencing downstream analysis pipelines, with both bulk and single-cell resolution, and the graphs that model repeated transcript structures for different biotypes. The software can be used as a python module or as a single-file executable program. CONCLUSIONS MGcount is a flexible total-RNA-seq quantification tool that successfully integrates reads that align to multiple genomic locations or that overlap with multiple gene features. Its approach is suitable for the simultaneous estimation of protein-coding, long non-coding and small non-coding transcript concentration, in both precursor and processed forms. Both source code and compiled software are available at https://github.com/hitaandrea/MGcount .
Collapse
Affiliation(s)
- Andrea Hita
- Epigenetics unit, Diagenode s.a., Liège, Belgium
- Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Ana Fernandez
- Epigenetics unit, Diagenode s.a., Liège, Belgium
- Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marc Rehmsmeier
- Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anna Alemany
- Department of Anatomy and Embryology, Leiden University Medical Centre, Leiden, The Netherlands
| | | |
Collapse
|
22
|
Bergeron D, Laforest C, Carpentier S, Calvé A, Fafard-Couture É, Deschamps-Francoeur G, Scott MS. SnoRNA copy regulation affects family size, genomic location and family abundance levels. BMC Genomics 2021; 22:414. [PMID: 34090325 PMCID: PMC8178906 DOI: 10.1186/s12864-021-07757-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/26/2021] [Indexed: 12/03/2022] Open
Abstract
Background Small nucleolar RNAs (snoRNAs) are an abundant class of noncoding RNAs present in all eukaryotes and best known for their involvement in ribosome biogenesis. In mammalian genomes, many snoRNAs exist in multiple copies, resulting from recombination and retrotransposition from an ancestral snoRNA. To gain insight into snoRNA copy regulation, we used Rfam classification and normal human tissue expression datasets generated using low structure bias RNA-seq to characterize snoRNA families. Results We found that although box H/ACA families are on average larger than box C/D families, the number of expressed members is similar for both types. Family members can cover a wide range of average abundance values, but importantly, expression variability of individual members of a family is preferred over the total variability of the family, especially for box H/ACA snoRNAs, suggesting that while members are likely differentially regulated, mechanisms exist to ensure uniformity of the total family abundance across tissues. Box C/D snoRNA family members are mostly embedded in the same host gene while box H/ACA family members tend to be encoded in more than one different host, supporting a model in which box C/D snoRNA duplication occurred mostly by cis recombination while box H/ACA snoRNA families have gained copy members through retrotransposition. And unexpectedly, snoRNAs encoded in the same host gene can be regulated independently, as some snoRNAs within the same family vary in abundance in a divergent way between tissues. Conclusions SnoRNA copy regulation affects family sizes, genomic location of the members and controls simultaneously member and total family abundance to respond to the needs of individual tissues. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07757-1.
Collapse
Affiliation(s)
- Danny Bergeron
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Cédric Laforest
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Stacey Carpentier
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Annabelle Calvé
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Étienne Fafard-Couture
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
| |
Collapse
|
23
|
Baldini L, Charpentier B, Labialle S. Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs. Noncoding RNA 2021; 7:ncrna7020030. [PMID: 34066559 PMCID: PMC8162545 DOI: 10.3390/ncrna7020030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Box C/D small nucleolar RNAs (C/D snoRNAs) represent an ancient family of small non-coding RNAs that are classically viewed as housekeeping guides for the 2′-O-methylation of ribosomal RNA in Archaea and Eukaryotes. However, an extensive set of studies now argues that they are involved in mechanisms that go well beyond this function. Here, we present these pieces of evidence in light of the current comprehension of the molecular mechanisms that control C/D snoRNA expression and function. From this inventory emerges that an accurate description of these activities at a molecular level is required to let the snoRNA field enter in a second age of maturity.
Collapse
Affiliation(s)
| | - Bruno Charpentier
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
| | - Stéphane Labialle
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
| |
Collapse
|
24
|
Fort RS, Duhagon MA. Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology. F1000Res 2021; 10:182. [PMID: 34354812 PMCID: PMC8287541 DOI: 10.12688/f1000research.28510.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/17/2022] Open
Abstract
Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (TCGA) Pan-Cancer cohort was estimated using the genome-wide DNA methylation and chromatin accessibility data (ATAC-seq) of their genes as surrogate variables. The association between vtRNA expression and patient clinical outcome, immune subtypes and transcriptionally co-regulated gene programs was analyzed in the dataset. Results: VtRNAs promoters are enriched in transcription factors related to viral infection. VtRNA2-1 is likely the most independently regulated homologue. VtRNA1-1 has the most accessible chromatin, followed by vtRNA1-2, vtRNA2-1 and vtRNA1-3. VtRNA1-1 and vtRNA1-3 chromatin status does not significantly change in cancer tissues. Meanwhile, vtRNA2-1 and vtRNA1-2 expression is widely deregulated in neoplastic tissues and its alteration is compatible with a broad oncogenic role for vtRNA1-2, and both tumor suppressor and oncogenic functions for vtRNA2-1. Yet, vtRNA1-1, vtRNA1-2 and vtRNA2-1 promoter DNA methylation predicts a shorter patient overall survival cancer-wide. In addition, gene ontology analyses of vtRNAs co-regulated genes identify a chromosome regulatory domain, epithelial differentiation, immune and thyroid cancer gene sets for specific vtRNAs. Furthermore, vtRNA expression patterns are associated with cancer immune subtypes and vtRNA1-2 expression is positively associated with cell proliferation and wound healing. Conclusions: Our study presents the landscape of vtRNA chromatin status cancer-wide, identifying co-regulated gene networks and ontological pathways associated with the different vtRNA genes that may account for their diverse roles in cancer.
Collapse
Affiliation(s)
- Rafael Sebastián Fort
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay.,Depto. de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Montevideo, 11600, Uruguay
| | - María Ana Duhagon
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay.,Depto. de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay
| |
Collapse
|
25
|
Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action. Biochem Soc Trans 2021; 48:645-656. [PMID: 32267490 PMCID: PMC7200641 DOI: 10.1042/bst20191046] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022]
Abstract
Identified five decades ago amongst the most abundant cellular RNAs, small nucleolar RNAs (snoRNAs) were initially described as serving as guides for the methylation and pseudouridylation of ribosomal RNA through direct base pairing. In recent years, however, increasingly powerful high-throughput genomic approaches and strategies have led to the discovery of many new members of the family and surprising diversity in snoRNA functionality and mechanisms of action. SnoRNAs are now known to target RNAs of many biotypes for a wider range of modifications, interact with diverse binding partners, compete with other binders for functional interactions, recruit diverse players to targets and affect protein function and accessibility through direct interaction. This mini-review presents the continuing characterization of the snoRNome through the identification of new snoRNA members and the discovery of their mechanisms of action, revealing a highly versatile noncoding family playing central regulatory roles and connecting the main cellular processes.
Collapse
|
26
|
Bousquet L, Hemon C, Malburet P, Bucchini F, Vandepoele K, Grimsley N, Moreau H, Echeverria M. The medium-size noncoding RNA transcriptome of Ostreococcus tauri, the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies. NAR Genom Bioinform 2020; 2:lqaa080. [PMID: 33575626 PMCID: PMC7671301 DOI: 10.1093/nargab/lqaa080] [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: 05/07/2020] [Revised: 08/31/2020] [Accepted: 09/17/2020] [Indexed: 11/14/2022] Open
Abstract
The small nucleolar RNAs (snoRNAs), essential for ribosome biogenesis, constitute a major family of medium-size noncoding RNAs (mncRNAs) in all eukaryotes. We present here, for the first time in a marine unicellular alga, the characterization of the snoRNAs family in Ostreococcus tauri, the smallest photosynthetic eukaryote. Using a transcriptomic approach, we identified 131 O. tauri snoRNAs (Ot–snoRNA) distributed in three classes: the C/D snoRNAs, the H/ACA snoRNAs and the MRP RNA. Their genomic organization revealed a unique combination of both the intronic organization of animals and the polycistronic organization of plants. Remarkably, clustered genes produced Ot–snoRNAs with unusual structures never previously described in plants. Their abundances, based on quantification of reads and northern blots, showed extreme differences in Ot–snoRNA accumulation, mainly determined by their differential stability. Most of these Ot–snoRNAs were predicted to target rRNAs or snRNAs. Seventeen others were orphan Ot–snoRNAs that would not target rRNA. These were specific to O. tauri or Mamiellophyceae and could have functions unrelated to ribosome biogenesis. Overall, these data reveal an ‘evolutionary response’ adapted to the extreme compactness of the O. tauri genome that accommodates the essential Ot–snoRNAs, developing multiple strategies to optimize their coordinated expression with a minimal cost on regulatory circuits.
Collapse
Affiliation(s)
- Laurie Bousquet
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
| | - Claire Hemon
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
| | - Paul Malburet
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
| | - François Bucchini
- Department of Plant Systems Biology,VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology,VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Bioinformatic Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Nigel Grimsley
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
| | - Hervé Moreau
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
| | - Manuel Echeverria
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Organismes Marins , UMR7232, F-66650 Banyuls sur Mer, France
- Département de Biologie, Université de Perpignan via Domitia, 66860 Perpignan Cedex, France
| |
Collapse
|
27
|
Sun Q, Song YJ, Prasanth KV. One locus with two roles: microRNA-independent functions of microRNA-host-gene locus-encoded long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1625. [PMID: 32945142 PMCID: PMC7965793 DOI: 10.1002/wrna.1625] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/22/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) are RNA transcripts longer than 200 nucleotides that do not code for proteins. LncRNAs play crucial regulatory roles in several biological processes via diverse mechanisms and their aberrant expression is associated with various diseases. LncRNA genes are further subcategorized based on their relative organization in the genome. MicroRNA (miRNA)-host-gene-derived lncRNAs (lnc-MIRHGs) refer to lncRNAs whose genes also harbor miRNAs. There exists crosstalk between the processing of lnc-MIRHGs and the biogenesis of the encoded miRNAs. Although the functions of the encoded miRNAs are usually well understood, whether those lnc-MIRHGs play independent functions are not fully elucidated. Here, we review our current understanding of lnc-MIRHGs, including their biogenesis, function, and mechanism of action, with a focus on discussing the miRNA-independent functions of lnc-MIRHGs, including their involvement in cancer. Our current understanding of lnc-MIRHGs strongly indicates that this class of lncRNAs could play important roles in basic cellular events as well as in diseases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
Collapse
Affiliation(s)
- Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
28
|
Robic A, Demars J, Kühn C. In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences. Cells 2020; 9:cells9081806. [PMID: 32751504 PMCID: PMC7464727 DOI: 10.3390/cells9081806] [Citation(s) in RCA: 8] [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: 04/29/2020] [Revised: 07/05/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
The sequencing of total RNA depleted for ribosomal sequences remains the method of choice for the study of circRNAs. Our objective was to characterize non-canonical circRNAs, namely not originating from back splicing and circRNA produced by non-coding genes. To this end, we analyzed a dataset from porcine testis known to contain about 100 intron-derived circRNAs. Labelling reads containing a circular junction and originating from back splicing provided information on the very small contribution of long non-coding genes to the production of canonical circRNAs. Analyses of the other reads revealed two origins for non-canonical circRNAs: (1) Intronic sequences for lariat-derived intronic circRNAs and intron circles, (2) Mono-exonic genes (mostly non-coding) for either a new type of circRNA (including only part of the exon: sub-exonic circRNAs) or, even more rarely, mono-exonic canonical circRNAs. The most complex set of sub-exonic circRNAs was produced by RNase_MRP (ribozyme RNA). We specifically investigated the intronic circRNA of ATXN2L, which is probably an independently transcribed sisRNA (stable intronic sequence RNA). We may be witnessing the emergence of a new non-coding gene in the porcine genome. Our results are evidence that most non-canonical circRNAs originate from non-coding sequences.
Collapse
Affiliation(s)
- Annie Robic
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France;
- Correspondence:
| | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France;
| | - Christa Kühn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany;
- Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
| |
Collapse
|
29
|
Yamaki Y, Nobe Y, Koike M, Yamauchi Y, Hirota K, Takahashi N, Nakayama H, Isobe T, Taoka M. Direct Determination of Pseudouridine in RNA by Mass Spectrometry Coupled with Stable Isotope Labeling. Anal Chem 2020; 92:11349-11356. [PMID: 32662983 DOI: 10.1021/acs.analchem.0c02122] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pseudouridine (Ψ) is the only "mass-silent" nucleoside produced by post-transcriptional RNA modification. We developed a mass spectrometry (MS)-based technique coupled with in vivo deuterium (D) labeling of uridines for direct determination of Ψs in cellular RNA and applied it to the comprehensive analysis of post-transcriptional modifications in human ribosomal RNAs. The method utilizes human TK6/mouse FM3A cells deficient in uridine monophosphate synthase using a CRISPR-Cas9 technique to turn off de novo uridine synthesis and fully labels uridines with D at uracil positions 5 and 6 by cultivating the cells in a medium containing uridine-5,6-D2. The pseudouridylation reaction in those cells results in the exchange of the D at the C5 of uracil with hydrogen from solvent, which produces a -1 Da mass shift, thus allowing MS-based determination of RNA Ψs. We present here the experimental details of this method and show that it allows the identification of all Ψs in human major nuclear and nucleolar RNAs, including several previously unknown Ψs. Because the method allows direct determination of Ψs at the femtomole level of RNA, it will serve as a useful tool for structure/function studies of a wide variety of noncoding RNAs.
Collapse
Affiliation(s)
- Yuka Yamaki
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Masami Koike
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Nobuhiro Takahashi
- Department of Biotechnology, Global Innovation Research Institute, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Hiroshi Nakayama
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| |
Collapse
|
30
|
Deschamps-Francoeur G, Simoneau J, Scott MS. Handling multi-mapped reads in RNA-seq. Comput Struct Biotechnol J 2020; 18:1569-1576. [PMID: 32637053 PMCID: PMC7330433 DOI: 10.1016/j.csbj.2020.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/06/2020] [Accepted: 06/07/2020] [Indexed: 11/07/2022] Open
Abstract
Many eukaryotic genomes harbour large numbers of duplicated sequences, of diverse biotypes, resulting from several mechanisms including recombination, whole genome duplication and retro-transposition. Such repeated sequences complicate gene/transcript quantification during RNA-seq analysis due to reads mapping to more than one locus, sometimes involving genes embedded in other genes. Genes of different biotypes have dissimilar levels of sequence duplication, with long-noncoding RNAs and messenger RNAs sharing less sequence similarity to other genes than biotypes encoding shorter RNAs. Many strategies have been elaborated to handle these multi-mapped reads, resulting in increased accuracy in gene/transcript quantification, although separate tools are typically used to estimate the abundance of short and long genes due to their dissimilar characteristics. This review discusses the mechanisms leading to sequence duplication, the biotypes affected, the computational strategies employed to deal with multi-mapped reads and the challenges that still remain to be overcome.
Collapse
Affiliation(s)
- Gabrielle Deschamps-Francoeur
- Département de Biochimie et Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Joël Simoneau
- Département de Biochimie et Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Michelle S. Scott
- Département de Biochimie et Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| |
Collapse
|
31
|
Boivin V, Reulet G, Boisvert O, Couture S, Elela SA, Scott MS. Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA. Nucleic Acids Res 2020; 48:2271-2286. [PMID: 31980822 PMCID: PMC7049693 DOI: 10.1093/nar/gkaa028] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 01/08/2020] [Accepted: 01/22/2020] [Indexed: 02/06/2023] Open
Abstract
The study of RNA expression is the fastest growing area of genomic research. However, despite the dramatic increase in the number of sequenced transcriptomes, we still do not have accurate estimates of the number and expression levels of non-coding RNA genes. Non-coding transcripts are often overlooked due to incomplete genome annotation. In this study, we use annotation-independent detection of RNA reads generated using a reverse transcriptase with low structure bias to identify non-coding RNA. Transcripts between 20 and 500 nucleotides were filtered and crosschecked with non-coding RNA annotations revealing 111 non-annotated non-coding RNAs expressed in different cell lines and tissues. Inspecting the sequence and structural features of these transcripts indicated that 60% of these transcripts correspond to new snoRNA and tRNA-like genes. The identified genes exhibited features of their respective families in terms of structure, expression, conservation and response to depletion of interacting proteins. Together, our data reveal a new group of RNA that are difficult to detect using standard gene prediction and RNA sequencing techniques, suggesting that reliance on actual gene annotation and sequencing techniques distorts the perceived architecture of the human transcriptome.
Collapse
Affiliation(s)
- Vincent Boivin
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Gaspard Reulet
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Olivier Boisvert
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sonia Couture
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| |
Collapse
|
32
|
Parenteau J, Abou Elela S. Introns: Good Day Junk Is Bad Day Treasure. Trends Genet 2019; 35:923-934. [PMID: 31668856 DOI: 10.1016/j.tig.2019.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/28/2019] [Accepted: 09/19/2019] [Indexed: 02/01/2023]
Abstract
Introns are ubiquitous in eukaryotic transcripts. They are often viewed as junk RNA but the huge energetic burden of transcribing, removing, and degrading them suggests a significant evolutionary advantage. Ostensibly, an intron functions within the host pre-mRNA to regulate its splicing, transport, and degradation. However, recent studies have revealed an entirely new class of trans-acting functions where the presence of intronic RNA in the cell impacts the expression of other genes in trans. Here, we review possible new mechanisms of intron functions, with a focus on the role of yeast introns in regulating the cell growth response to starvation.
Collapse
Affiliation(s)
- Julie Parenteau
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| |
Collapse
|
33
|
Boivin V, Faucher-Giguère L, Scott M, Abou-Elela S. The cellular landscape of mid-size noncoding RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1530. [PMID: 30843375 PMCID: PMC6619189 DOI: 10.1002/wrna.1530] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/06/2023]
Abstract
Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid-size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes. Many are found in multiple copies in genomes. mncRNAs are highly structured and carry many posttranscriptional modifications. Both of these facets dictate their RNA-binding protein partners and ultimately their function. mncRNAs have already been implicated in translation, catalysis, as guides for RNA modification, as spliceosome components and regulatory RNA. However, recent studies are adding new mncRNA functions including regulation of gene expression and alternative splicing. In this review, we describe the different classes, characteristics and emerging functions of mncRNAs and their relative expression patterns. Finally, we provide a portrait of the challenges facing their detection and annotation in databases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
Collapse
Affiliation(s)
- Vincent Boivin
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Laurence Faucher-Giguère
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Michelle Scott
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sherif Abou-Elela
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| |
Collapse
|