1
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Wu HYL, Ai Q, Teixeira RT, Nguyen PHT, Song G, Montes C, Elmore JM, Walley JW, Hsu PY. Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis. THE PLANT CELL 2024; 36:510-539. [PMID: 38000896 PMCID: PMC10896292 DOI: 10.1093/plcell/koad290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/26/2023]
Abstract
A crucial step in functional genomics is identifying actively translated ORFs and linking them to biological functions. The challenge lies in identifying short ORFs, as their identification is greatly influenced by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis (Arabidopsis thaliana), revealing uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. Assisted by a transcriptome assembly, we identified 7,751 unconventional translation events, comprising 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ORFs in presumed noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events. We present evidence of active translation from primary transcripts of trans-acting small interfering RNAs (TAS1-4) and microRNAs (pri-MIR163 and pri-MIR169) and periodic ribosome stalling supporting cotranslational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORFs (AUG-stop), and 2,921 tiny uORFs (2 to 10 amino acids) and 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as do longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaoyun Ai
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Rita Teresa Teixeira
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Phong H T Nguyen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Gaoyuan Song
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - J Mitch Elmore
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Justin W Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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2
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Montagud‐Martínez R, Márquez‐Costa R, Heras‐Hernández M, Dolcemascolo R, Rodrigo G. On the ever-growing functional versatility of the CRISPR-Cas13 system. Microb Biotechnol 2024; 17:e14418. [PMID: 38381083 PMCID: PMC10880580 DOI: 10.1111/1751-7915.14418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
CRISPR-Cas systems evolved in prokaryotes to implement a powerful antiviral immune response as a result of sequence-specific targeting by ribonucleoproteins. One of such systems consists of an RNA-guided RNA endonuclease, known as CRISPR-Cas13. In very recent years, this system is being repurposed in different ways in order to decipher and engineer gene expression programmes. Here, we discuss the functional versatility of the CRISPR-Cas13 system, which includes the ability for RNA silencing, RNA editing, RNA tracking, nucleic acid detection and translation regulation. This functional palette makes the CRISPR-Cas13 system a relevant tool in the broad field of systems and synthetic biology.
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Affiliation(s)
- Roser Montagud‐Martínez
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Rosa Márquez‐Costa
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - María Heras‐Hernández
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Roswitha Dolcemascolo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
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3
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Backofen R, Gorodkin J, Hofacker IL, Stadler PF. Comparative RNA Genomics. Methods Mol Biol 2024; 2802:347-393. [PMID: 38819565 DOI: 10.1007/978-1-0716-3838-5_12] [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] [Indexed: 06/01/2024]
Abstract
Over the last quarter of a century it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large-scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible non-coding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of non-coding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.
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Affiliation(s)
- Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Jan Gorodkin
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria
- Bioinformatics and Computational Biology research group, University of Vienna, Vienna, Austria
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany.
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
- Universidad National de Colombia, Bogotá, Colombia.
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria.
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.
- Santa Fe Institute, Santa Fe, NM, USA.
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4
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Liang Y, Xu H, Cheng T, Fu Y, Huang H, Qian W, Wang J, Zhou Y, Qian P, Yin Y, Xu P, Zou W, Chen B. Gene activation guided by nascent RNA-bound transcription factors. Nat Commun 2022; 13:7329. [PMID: 36443367 PMCID: PMC9705438 DOI: 10.1038/s41467-022-35041-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022] Open
Abstract
Technologies for gene activation are valuable tools for the study of gene functions and have a wide range of potential applications in bioengineering and medicine. In contrast to existing methods based on recruiting transcriptional modulators via DNA-binding proteins, we developed a strategy termed Narta (nascent RNA-guided transcriptional activation) to achieve gene activation by recruiting artificial transcription factors (aTFs) to transcription sites through nascent RNAs of the target gene. Using Narta, we demonstrate robust activation of a broad range of exogenous and endogenous genes in various cell types, including zebrafish embryos, mouse and human cells. Importantly, the activation is reversible, tunable and specific. Moreover, Narta provides better activation potency of some expressed genes than CRISPRa and, when used in combination with CRISPRa, has an enhancing effect on gene activation. Quantitative imaging illustrated that nascent RNA-directed aTFs could induce the high-density assembly of coactivators at transcription sites, which may explain the larger transcriptional burst size induced by Narta. Overall, our work expands the gene activation toolbox for biomedical research.
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Affiliation(s)
- Ying Liang
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China ,grid.13402.340000 0004 1759 700XLiangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Haiyue Xu
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China ,grid.13402.340000 0004 1759 700XLiangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Tao Cheng
- grid.13402.340000 0004 1759 700XWomen’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yujuan Fu
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hanwei Huang
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenchang Qian
- grid.13402.340000 0004 1759 700XCenter of Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Junyan Wang
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuenan Zhou
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Pengxu Qian
- grid.13402.340000 0004 1759 700XCenter of Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yafei Yin
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Pengfei Xu
- grid.13402.340000 0004 1759 700XWomen’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Zou
- grid.13402.340000 0004 1759 700XThe Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China ,grid.13402.340000 0004 1759 700XInsititute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Baohui Chen
- grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China ,grid.13402.340000 0004 1759 700XLiangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China ,grid.13402.340000 0004 1759 700XInstitute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China ,grid.13402.340000 0004 1759 700XZhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China
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5
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Abu-Elmagd M, Assidi M, Alrefaei AF, Rebai A. Editorial: Advances in genomic and genetic tools, and their applications for understanding embryonic development and human diseases. Front Cell Dev Biol 2022; 10:1016400. [PMID: 36478744 PMCID: PMC9720382 DOI: 10.3389/fcell.2022.1016400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/04/2022] [Indexed: 10/10/2023] Open
Abstract
Significant advances have been recently made in the development of the genetic and genomic platforms. This has greatly contributed to a better understanding of gene expression and regulation machinery. Consequently, this led to considerable progress in unraveling evidence of the genotype-phenotype correlation between normal/abnormal embryonic development and human disease complexity. For example, advanced genomic tools such as next-generation sequencing, and microarray-based CGH have substantially helped in the identification of gene and copy number variants associated with diseases as well as in the discovery of causal gene mutations. In addition, bioinformatic analysis tools of genome annotation and comparison have greatly aided in data analysis for the interpretation of the genetic variants at the individual level. This has unlocked potential possibilities for real advances toward new therapies in personalized medicine for the targeted treatment of human diseases. However, each of these genomic and bioinformatics tools has its limitations and hence further efforts are required to implement novel approaches to overcome these limitations. It could be possible that the use of more than one platform for genotype-phenotype deep analysis is an effective approach to disentangling the cause and treatment of the disease complexities. Our research topic aimed at deciphering these complexities by shedding some light on the recent applications of the basic and advanced genetic/genomic and bioinformatics approaches. These include studying gene-gene, protein-protein, and gene-environment interactions. We, in addition, aimed at a better understanding of the link between normal/abnormal embryonic development and the cause of human disease induction.
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Affiliation(s)
- Muhammad Abu-Elmagd
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulmajeed F. Alrefaei
- Department of Biology, Jamoum University College, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Ahmed Rebai
- Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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6
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Sruthi KB, Menon A, P A, Vasudevan Soniya E. Pervasive translation of small open reading frames in plant long non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2022; 13:975938. [PMID: 36352887 PMCID: PMC9638090 DOI: 10.3389/fpls.2022.975938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) are primarily recognized as non-coding transcripts longer than 200 nucleotides with low coding potential and are present in both eukaryotes and prokaryotes. Recent findings reveal that lncRNAs can code for micropeptides in various species. Micropeptides are generated from small open reading frames (smORFs) and have been discovered frequently in short mRNAs and non-coding RNAs, such as lncRNAs, circular RNAs, and pri-miRNAs. The most accepted definition of a smORF is an ORF containing fewer than 100 codons, and ribosome profiling and mass spectrometry are the most prevalent experimental techniques used to identify them. Although the majority of micropeptides perform critical roles throughout plant developmental processes and stress conditions, only a handful of their functions have been verified to date. Even though more research is being directed toward identifying micropeptides, there is still a dearth of information regarding these peptides in plants. This review outlines the lncRNA-encoded peptides, the evolutionary roles of such peptides in plants, and the techniques used to identify them. It also describes the functions of the pri-miRNA and circRNA-encoded peptides that have been identified in plants.
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7
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Butz H. Circulating Noncoding RNAs in Pituitary Neuroendocrine Tumors-Two Sides of the Same Coin. Int J Mol Sci 2022; 23:ijms23095122. [PMID: 35563510 PMCID: PMC9101693 DOI: 10.3390/ijms23095122] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 01/27/2023] Open
Abstract
Pituitary neuroendocrine tumors (PitNET) are common intracranial neoplasms. While in case of hormone secreting tumors pituitary hormone measurements can be used for monitoring the disease, in non-functional tumors there is a need to discover non-invasive biomarkers. Non-coding RNAs (ncRNAs) are popular biomarker candidates due to their stability and tissue specificity. Among ncRNAs, miRNAs, lncRNAs and circRNAs have been investigated the most in pituitary tumor tissues and in circulation. However, it is still not known whether ncRNAs are originated from the pituitary, or whether they are casually involved in the pathophysiology. Additionally, there is strong diversity among different studies reporting ncRNAs in PitNET. Therefore, to provide an overview of the discrepancies between published studies and to uncover the reasons why despite encouraging experimental data application of ncRNAs in clinical routine has not yet taken hold, in this review available data are summarized on circulating ncRNAs in PitNET. The data on circulating miRNAs, lncRNAs and circRNAs are organized according to different PitNET subtypes. Biological (physiological and pathophysiological) factors behind intra- and interindividual variability and technical aspects of detecting these markers, including preanalytical and analytical parameters, sample acquisition (venipuncture) and type, storage, nucleic acid extraction, quantification and normalization, which reveal the two sides of the same coin are discussed.
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Affiliation(s)
- Henriett Butz
- Hereditary Tumours Research Group, Hungarian Academy of Sciences-Semmelweis University, H-1089 Budapest, Hungary;
- Department of Laboratory Medicine, Semmelweis University, H-1089 Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, H-1122 Budapest, Hungary
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8
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Context-Dependent Regulation of Gene Expression by Non-Canonical Small RNAs. Noncoding RNA 2022; 8:ncrna8030029. [PMID: 35645336 PMCID: PMC9149963 DOI: 10.3390/ncrna8030029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
In recent functional genomics studies, a large number of non-coding RNAs have been identified. It has become increasingly apparent that noncoding RNAs are crucial players in a wide range of cellular and physiological functions. They have been shown to modulate gene expression on different levels, including transcription, post-transcriptional processing, and translation. This review aims to highlight the diverse mechanisms of the regulation of gene expression by small noncoding RNAs in different conditions and different types of human cells. For this purpose, various cellular functions of microRNAs (miRNAs), circular RNAs (circRNAs), snoRNA-derived small RNAs (sdRNAs) and tRNA-derived fragments (tRFs) will be exemplified, with particular emphasis on the diversity of their occurrence and on the effects on gene expression in different stress conditions and diseased cell types. The synthesis and effect on gene expression of these noncoding RNAs varies in different cell types and may depend on environmental conditions such as different stresses. Moreover, noncoding RNAs play important roles in many diseases, including cancer, neurodegenerative disorders, and viral infections.
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9
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Zuo Q, Jing J, Zhou J, Zhang Y, Wei W, Chen G, Li B. Dual regulatory actions of LncBMP4 on BMP4 promote chicken primordial germ cell formation. EMBO Rep 2022; 23:e52491. [PMID: 34747116 PMCID: PMC8728602 DOI: 10.15252/embr.202152491] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/22/2021] [Accepted: 10/18/2021] [Indexed: 01/07/2023] Open
Abstract
The unique characteristics of chicken primordial germ cells (PGCs) provide potential strategies for transgenic animal generation; however, insufficient PGC availability has limited their application. Regulation of bone morphogenic protein 4 (BMP4), a crucial factor for PGCs formation, may provide new strategies for PGC generation. We here identify a long noncoding RNA (lncRNA) that targets BMP4 (LncBMP4). LncBMP4 has similar functions as BMP4, in that it facilitates the formation and migration of PGCs. LncBMP4 promotes BMP4 expression by adsorbing the miRNA gga-mir-12211, thus reducing its inhibitory effect on BMP4 expression. In addition, the small peptide EPC5 encoded by LncBMP4 promotes the transcription of BMP4. The competing endogenous RNA (ceRNA) effect of LncBMP4 requires N6-methyladenosine (m6A) modification, in a dose-dependent manner, and high levels of m6A modification hinder EPC5 translation. Understanding the molecular mechanisms through which LncBMP4 promotes BMP4 expression during PGC formation may provide new avenues for efficient PGC generation.
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Affiliation(s)
- Qisheng Zuo
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Jin Jing
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Jing Zhou
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Yani Zhang
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Wanhong Wei
- Department of Biological SciencesCollege of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Bichun Li
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
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10
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Long noncoding RNAs profiling in ovary during laying and nesting in Muscovy ducks (Cairina moschata). Anim Reprod Sci 2021; 230:106762. [PMID: 34022609 DOI: 10.1016/j.anireprosci.2021.106762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 05/01/2021] [Accepted: 05/03/2021] [Indexed: 12/11/2022]
Abstract
There are recent reports of the important functions of long noncoding RNAs (lncRNAs) in female reproductive and ovarian development. Studies in which there was characterization of lncRNAs in the ovaries of laying compared with nesting poultry, however, are limited. In this study, RNA libraries were constructed by obtaining sequencing data of ovarian tissues from laying and nesting Muscovy ducks. In the ovarian tissues of Muscovy ducks, a total of 334 differentially abundant mRNA transcripts (DEGs) and 36 differentially abundant lncRNA transcripts were identified in the nesting period, when compared with during the laying period. These results were subsequently validated by qRT-PCR using nine randomly-selected lncRNAs and six randomly-selected DAMTs. Furthermore, the cis- and trans-regulatory target genes of differentially abundant lncRNA transcripts were identified, and lncRNA-gene interaction networks of 34 differentially abundant lncRNAs and 263 DEGs were constructed. A total of 7601 lncRNAs neighboring 10,542 protein-coding genes were identified and found to be enriched in the Wnt signaling pathway and oocyte meiosis pathways associated with follicular development. Overall, only 11 cis-targets and 57 mRNA-mRNA except trans-targets were involved in the lncRNA-gene interaction networks. Based on the interaction networks, nine DEGs were trans-regulated by differentially abundant lncRNAs and 20 differentially abundant lncRNAs were hypothesized to have important functions in the regulation of broodiness in Muscovy ducks. In this study, a predicted interaction network of differentially abundant lncRNAs and DEGs in Muscovy ducks was constructed for the first time leading to an enhanced understanding of lncRNA and gene interactions regulating broodiness.
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11
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Plasek LM, Valadkhan S. lncRNAs in T lymphocytes: RNA regulation at the heart of the immune response. Am J Physiol Cell Physiol 2021; 320:C415-C427. [PMID: 33296288 PMCID: PMC8294623 DOI: 10.1152/ajpcell.00069.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genome-wide analyses in the last decade have uncovered the presence of a large number of long non-protein-coding transcripts that show highly tissue- and state-specific expression patterns. High-throughput sequencing analyses in diverse subsets of immune cells have revealed a complex and dynamic expression pattern for these long noncoding RNAs (lncRNAs) that correlate with the functional states of immune cells. Although the vast majority of lncRNAs expressed in immune cells remain unstudied, functional studies performed on a small subset have indicated that their state-specific expressions pattern frequently has a regulatory impact on the function of immune cells. In vivo and in vitro studies have pointed to the involvement of lncRNAs in a wide variety of cellular processes, including both the innate and adaptive immune response through mechanisms ranging from epigenetic and transcriptional regulation to sequestration of functional molecules in subcellular compartments. This review will focus mainly on the role of lncRNAs in CD4+ and CD8+ T cells, which play pivotal roles in adaptive immunity. Recent studies have pointed to key physiological functions for lncRNAs during several developmental and functional stages of the life cycle of lymphocytes. Although lncRNAs play important physiological roles in lymphocytic response to antigenic stimulation, differentiation into effector cells, and secretion of cytokines, their dysregulated expression can promote or sustain pathological states such as autoimmunity, chronic inflammation, cancer, and viremia. This, together with their highly cell type-specific expression patterns, makes lncRNAs ideal therapeutic targets and underscores the need for additional studies into the role of these understudied transcripts in adaptive immune response.
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12
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Huang Y, Wang J, Zhao Y, Wang H, Liu T, Li Y, Cui T, Li W, Feng Y, Luo J, Gong J, Ning L, Zhang Y, Wang D, Zhang Y. cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function. Nucleic Acids Res 2021; 49:D65-D70. [PMID: 33010163 PMCID: PMC7778915 DOI: 10.1093/nar/gkaa791] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/30/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
RNA endowed with both protein-coding and noncoding functions is referred to as 'dual-function RNA', 'binary functional RNA (bifunctional RNA)' or 'cncRNA (coding and noncoding RNA)'. Recently, an increasing number of cncRNAs have been identified, including both translated ncRNAs (ncRNAs with coding functions) and untranslated mRNAs (mRNAs with noncoding functions). However, an appropriate database for storing and organizing cncRNAs is still lacking. Here, we developed cncRNAdb, a manually curated database of experimentally supported cncRNAs, which aims to provide a resource for efficient manipulation, browsing and analysis of cncRNAs. The current version of cncRNAdb documents about 2600 manually curated entries of cncRNA functions with experimental evidence, involving more than 2,000 RNAs (including over 1300 translated ncRNAs and over 600 untranslated mRNAs) across over 20 species. In summary, we believe that cncRNAdb will help elucidate the functions and mechanisms of cncRNAs and develop new prediction methods. The database is available at http://www.rna-society.org/cncrnadb/.
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MESH Headings
- 3' Untranslated Regions
- 5' Untranslated Regions
- Animals
- Databases, Nucleic Acid/organization & administration
- Drosophila melanogaster/genetics
- Humans
- Mice
- MicroRNAs/classification
- MicroRNAs/genetics
- Pan troglodytes/genetics
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Messenger/classification
- RNA, Messenger/genetics
- RNA, Ribosomal/classification
- RNA, Ribosomal/genetics
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Transfer/classification
- RNA, Transfer/genetics
- Software
- Zebrafish/genetics
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Affiliation(s)
- Yan Huang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Jing Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yue Zhao
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310053, China
| | - Huafeng Wang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Tianyuan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuhe Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Weiyi Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yige Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaqi Gong
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yong Zhang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Dong Wang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yang Zhang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
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13
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Bogard B, Francastel C, Hubé F. Multiple information carried by RNAs: total eclipse or a light at the end of the tunnel? RNA Biol 2020; 17:1707-1720. [PMID: 32559119 PMCID: PMC7714488 DOI: 10.1080/15476286.2020.1783868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/06/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
The findings that an RNA is not necessarily either coding or non-coding, or that a precursor RNA can produce different types of mature RNAs, whether coding or non-coding, long or short, have challenged the dichotomous view of the RNA world almost 15 years ago. Since then, and despite an increasing number of studies, the diversity of information that can be conveyed by RNAs is rarely searched for, and when it is known, it remains largely overlooked in further functional studies. Here, we provide an update with prominent examples of multiple functions that are carried by the same RNA or are produced by the same precursor RNA, to emphasize their biological relevance in most living organisms. An important consequence is that the overall function of their locus of origin results from the balance between various RNA species with distinct functions and fates. The consideration of the molecular basis of this multiplicity of information is obviously crucial for downstream functional studies when the targeted functional molecule is often not the one that is believed.
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Affiliation(s)
- Baptiste Bogard
- Université De Paris, Epigenetics and Cell Fate, CNRS, Paris, France
| | | | - Florent Hubé
- Université De Paris, Epigenetics and Cell Fate, CNRS, Paris, France
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14
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Das T, Deb A, Parida S, Mondal S, Khatua S, Ghosh Z. LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients. RNA Biol 2020; 18:1136-1151. [PMID: 33112702 DOI: 10.1080/15476286.2020.1833529] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and C.elegans. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at http://dibresources.jcbose.ac.in/zhumur/lncrbase2/.
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Affiliation(s)
- Troyee Das
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Aritra Deb
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sibun Parida
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sudip Mondal
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Sunirmal Khatua
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
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15
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Towards a comprehensive pipeline to identify and functionally annotate long noncoding RNA (lncRNA). Comput Biol Med 2020; 127:104028. [PMID: 33126123 DOI: 10.1016/j.compbiomed.2020.104028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/20/2022]
Abstract
Long noncoding RNAs (lncRNAs) are implicated in various genetic diseases and cancer, attributed to their critical role in gene regulation. They are a divergent group of RNAs and are easily differentiated from other types with unique characteristics, functions, and mechanisms of action. In this review, we provide a list of some of the prominent data repositories containing lncRNAs, their interactome, and predicted and validated disease associations. Next, we discuss various wet-lab experiments formulated to obtain the data for these repositories. We also provide a critical review of in silico methods available for the identification purpose and suggest techniques to further improve their performance. The bulk of the methods currently focus on distinguishing lncRNA transcripts from the coding ones. Functional annotation of these transcripts still remains a grey area and more efforts are needed in that space. Finally, we provide details of current progress, discuss impediments, and illustrate a roadmap for developing a generalized computational pipeline for comprehensive annotation of lncRNAs, which is essential to accelerate research in this area.
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16
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Choi SW, Kim HW, Nam JW. The small peptide world in long noncoding RNAs. Brief Bioinform 2020; 20:1853-1864. [PMID: 30010717 PMCID: PMC6917221 DOI: 10.1093/bib/bby055] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/08/2018] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a group of transcripts that are longer than 200 nucleotides (nt) without coding potential. Over the past decade, tens of thousands of novel lncRNAs have been annotated in animal and plant genomes because of advanced high-throughput RNA sequencing technologies and with the aid of coding transcript classifiers. Further, a considerable number of reports have revealed the existence of stable, functional small peptides (also known as micropeptides), translated from lncRNAs. In this review, we discuss the methods of lncRNA classification, the investigations regarding their coding potential and the functional significance of the peptides they encode.
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Affiliation(s)
- Seo-Won Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Hyun-Woo Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
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17
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Ito KK, Watanabe K, Kitagawa D. The Emerging Role of ncRNAs and RNA-Binding Proteins in Mitotic Apparatus Formation. Noncoding RNA 2020; 6:E13. [PMID: 32245090 PMCID: PMC7151635 DOI: 10.3390/ncrna6010013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 12/14/2022] Open
Abstract
Mounting experimental evidence shows that non-coding RNAs (ncRNAs) serve a wide variety of biological functions. Recent studies suggest that a part of ncRNAs are critically important for supporting the structure of subcellular architectures. Here, we summarize the current literature demonstrating the role of ncRNAs and RNA-binding proteins in regulating the assembly of mitotic apparatus, especially focusing on centrosomes, kinetochores, and mitotic spindles.
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Affiliation(s)
| | | | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan; (K.K.I.); (K.W.)
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18
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A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs. Int J Mol Sci 2020; 21:ijms21010302. [PMID: 31906285 PMCID: PMC6982300 DOI: 10.3390/ijms21010302] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
In late 2012 it was evidenced that most of the human genome is transcribed but only a small percentage of the transcripts are translated. This observation supported the importance of non-coding RNAs and it was confirmed in several organisms. The most abundant non-translated transcripts are long non-coding RNAs (lncRNAs). In contrast to protein-coding RNAs, they show a more cell-specific expression. To understand the function of lncRNAs, it is fundamental to investigate in which cells they are preferentially expressed and to detect their subcellular localization. Recent improvements of techniques that localize single RNA molecules in tissues like single-cell RNA sequencing and fluorescence amplification methods have given a considerable boost in the knowledge of the lncRNA functions. In recent years, single-cell transcription variability was associated with non-coding RNA expression, revealing this class of RNAs as important transcripts in the cell lineage specification. The purpose of this review is to collect updated information about lncRNA classification and new findings on their function derived from single-cell analysis. We also retained useful for all researchers to describe the methods available for single-cell analysis and the databases collecting single-cell and lncRNA data. Tables are included to schematize, describe, and compare exposed concepts.
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19
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Mewalal R, Yin H, Hu R, Jawdy S, Vion P, Tuskan GA, Le Tacon F, Labbé JL, Yang X. Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis. Front Microbiol 2019; 10:515. [PMID: 30936859 PMCID: PMC6431645 DOI: 10.3389/fmicb.2019.00515] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 02/28/2019] [Indexed: 12/02/2022] Open
Abstract
Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth. A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant:microbe-based strategies. These beneficial associations entail extensive morphological changes orchestrated by the genetic reprogramming in both organisms. In this study, we performed a comparative analysis of two Populus species (Populus deltoides and P. trichocarpa) that were colonized by either an arbuscular mycorrhizal fungus (AmF), Rhizophagus irregularis or an ectomycorrhizal fungus (EmF), Laccaria bicolor, to describe the small RNA (sRNA) landscape including small open reading frames (sORFs) and micro RNAs (miRNAs) involved in these mutualistic interactions. We identified differential expression of sRNAs that were, to a large extent, (1) within the genomic regions lacking annotated genes in the Populus genome and (2) distinct for each fungal interaction. These sRNAs may be a source of novel sORFs within a genome, and in this regard, we identified potential sORFs encoded by the sRNAs. We predicted a higher number of differentially-expressed miRNAs in P. trichocarpa (4 times more) than in P. deltoides (conserved and novel). In addition, 44 miRNAs were common in P. trichocarpa between the EmF and AmF treatments, and only 4 miRNAs were common in P. deltoides between the treatments. Root colonization by either fungus was more effective in P. trichocarpa than in P. deltoides, thus the relatively few differentially-expressed miRNAs predicted in P. deltoides might reflect the extent of the symbiosis. Finally, we predicted several genes targets for the plant miRNAs identified here, including potential fungal gene targets. Our findings shed light on additional molecular tiers with a role in Populus-fungal mutualistic associations and provides a set of potential molecular targets for future enhancement.
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Affiliation(s)
- Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Patrice Vion
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, VandIJuvre-lès-Nancy, France
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - François Le Tacon
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, VandIJuvre-lès-Nancy, France
| | - Jessy L. Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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20
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Zhang X, Shi J, Sun Y, Zhu Y, Zhang Z, Wang Y. Transcriptome analysis provides insights into differentially expressed genes and long noncoding RNAs involved in sex‐related differences in Amur sturgeon (
Acipenser schrenckii
). Mol Reprod Dev 2018; 86:132-144. [DOI: 10.1002/mrd.23065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/05/2018] [Indexed: 01/31/2023]
Affiliation(s)
- Xin Zhang
- Department of Aquaculture, College of Animal Science, Fujian Agriculture and Forestry UniversityFuzhou China
| | - Jialong Shi
- Department of Aquaculture, College of Animal Science, Fujian Agriculture and Forestry UniversityFuzhou China
| | - Yulong Sun
- Department of Aquaculture, College of Animal Science, Fujian Agriculture and Forestry UniversityFuzhou China
| | - Youfang Zhu
- Department of Aquaculture, Putian Municipal Institute of Fisheries ResearchPutian China
| | - Ziping Zhang
- Department of Aquaculture, College of Animal Science, Fujian Agriculture and Forestry UniversityFuzhou China
| | - Yilei Wang
- Department of Aquaculture, Fisheries College, Jimei UniversityXiamen China
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21
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Sheng L, Ye L, Zhang D, Cawthorn WP, Xu B. New Insights Into the Long Non-coding RNA SRA: Physiological Functions and Mechanisms of Action. Front Med (Lausanne) 2018; 5:244. [PMID: 30238005 PMCID: PMC6135885 DOI: 10.3389/fmed.2018.00244] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNA) are emerging as new genetic/epigenetic regulators that can impact almost all physiological functions. Here, we focus on the long non-coding steroid receptor RNA activator (SRA), including new insights into its effects on gene expression, the cell cycle, and differentiation; how these relate to physiology and disease; and the mechanisms underlying these effects. We discuss how SRA acts as an RNA coactivator in nuclear receptor signaling; its effects on steroidogenesis, adipogenesis, and myocyte differentiation; the impact on breast and prostate cancer tumorigenesis; and, finally, its ability to modulate hepatic steatosis through several signaling pathways. Genome-wide analysis reveals that SRA regulates hundreds of target genes in adipocytes and breast cancer cells and binds to thousands of genomic sites in human pluripotent stem cells. Recent studies indicate that SRA acts as a molecular scaffold and forms networks with numerous coregulators and chromatin-modifying regulators in both activating and repressive complexes. We discuss how modifications to SRA's unique stem-loop secondary structure are important for SRA function, and highlight the various SRA isoforms and mutations that have clinical implications. Finally, we discuss the future directions for better understanding the molecular mechanisms of SRA action and how this might lead to new diagnostic and therapeutic approaches.
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Affiliation(s)
- Liang Sheng
- Department of Pharmacology, School of Basic Medical Science, Nanjing Medical University, Nanjing, China.,Neuroprotective Drug Discovery Key Laboratory of Nanjing Medical University, Nanjing, China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Dong Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - William P Cawthorn
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Bin Xu
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan Medical Center Ann Arbor, MI, United States
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22
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Valadkhan S, Plasek LM. Long Non-Coding RNA-Mediated Regulation of the Interferon Response: A New Perspective on a Familiar Theme. Pathog Immun 2018. [PMID: 30135954 PMCID: PMC6101671 DOI: 10.20411/pai.v3i1.252] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The interferon (IFN) response is a critical and ubiquitous component of the innate immune response to pathogens. Detailed studies in the last decades have elucidated the function of a large number of proteins that mediate the complex signaling pathways and gene expression programs involved in the interferon response. The recent discovery of the long non-coding RNAs (lncRNAs) as a new category of cellular effectors has led to studies aiming to understand the role of these transcripts in the IFN response. Several high throughput studies have shown that a large number of lncRNAs are differentially expressed following IFN stimulation and/or viral infections. In-depth study of a very small fraction of the identified lncRNAs has revealed critical roles for this class of transcripts in the regulation of multiple steps of the IFN response, and pointed to the presence of an extensive RNA-mediated regulatory network during the antiviral response. As the vast majority of the identified potential regulatory lncRNAs remain unstudied, it is highly likely that future studies will reveal a completely new perspective on the regulation of the IFN response, with lncRNA- and protein-mediated regulatory networks coordinating the duration, magnitude, and character of this aspect of the innate immune response. In addition to providing a more complete picture of the IFN response, these studies will likely identify new therapeutic targets that in the long term may impact the therapeutic options available against microbial infections and diseases of the immune system.
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Affiliation(s)
- Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Leah M Plasek
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
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23
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Hubé F, Francastel C. Coding and Non-coding RNAs, the Frontier Has Never Been So Blurred. Front Genet 2018; 9:140. [PMID: 29720998 PMCID: PMC5915474 DOI: 10.3389/fgene.2018.00140] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/04/2018] [Indexed: 11/25/2022] Open
Affiliation(s)
- Florent Hubé
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, Centre National de la Recherche Scientifique UMR7216, Paris, France
| | - Claire Francastel
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, Centre National de la Recherche Scientifique UMR7216, Paris, France
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24
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Choi SW, Nam JW. TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association. BMC Bioinformatics 2018; 19:41. [PMID: 29504902 PMCID: PMC5836835 DOI: 10.1186/s12859-018-2013-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND LncRNAs are long regulatory non-coding RNAs, some of which are arguably predicted to have coding potential. Despite coding potential classifiers that utilize ribosome profiling data successfully detected actively translated regions, they are less sensitive to lncRNAs. Furthermore, lncRNA annotation can be susceptible to false positives obtained from 3' untranslated region (UTR) fragments of mRNAs. RESULTS To lower these limitations in lncRNA annotation, we present a novel tool TERIUS that provides a two-step filtration process to distinguish between bona fide and false lncRNAs. The first step successfully separates lncRNAs from protein-coding genes showing enhanced sensitivity compared to other methods. To eliminate 3'UTR fragments, the second step takes advantage of the 3'UTR-specific association with regulator of nonsense transcripts 1 (UPF1), leading to refined lncRNA annotation. Importantly, TERIUS enabled the detection of misclassified transcripts in published lncRNA annotations. CONCLUSIONS TERIUS is a robust method for lncRNA annotation, which provides an additional filtration step for 3'UTR fragments. TERIUS was able to successfully re-classify GENCODE and miTranscriptome lncRNA annotations. We believe that TERIUS can benefit construction of extensive and accurate non-coding transcriptome maps in many genomes.
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Affiliation(s)
- Seo-Won Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea. .,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
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25
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Abstract
Over the last two decades it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of noncoding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.
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Affiliation(s)
- Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany.,Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
| | - Ivo L Hofacker
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.,Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.,Bioinformatics and Computational Biology Research Group, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
| | - Peter F Stadler
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark. .,Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria. .,Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany. .,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany. .,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany. .,Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA.
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26
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Mehra M, Chauhan R. Long Noncoding RNAs as a Key Player in Hepatocellular Carcinoma. BIOMARKERS IN CANCER 2017; 9:1179299X17737301. [PMID: 29147078 PMCID: PMC5673005 DOI: 10.1177/1179299x17737301] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Indexed: 12/16/2022]
Abstract
Hepatocellular carcinoma (HCC) is a major malignancy in the liver and has emerged as one of the main cancers in the world with a high mortality rate. However, the molecular mechanisms of HCC are still poorly understood. Long noncoding RNAs (lncRNAs) have recently come to the forefront as functional non-protein-coding RNAs that are involved in a variety of cellular processes ranging from maintaining the structural integrity of chromosomes to gene expression regulation in a spatiotemporal manner. Many recent studies have reported the involvement of lncRNAs in HCC which has led to a better understanding of the underlying molecular mechanisms operating in HCC. Long noncoding RNAs have been shown to regulate development and progression of HCC, and thus, lncRNAs have both diagnostic and therapeutic potentials. In this review, we present an overview of the lncRNAs involved in different stages of HCC and their potential in clinical applications which have been studied so far.
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Affiliation(s)
- Mrigaya Mehra
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
- Academy of Scientific & Innovative Research, Chennai, India
| | - Ranjit Chauhan
- Department of Hepatology, Loyola University Chicago, Chicago, IL, USA
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Health Sciences Center, Memorial University, St John’s, Newfoundland and Labrador, Canada
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27
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Hsu PY, Benfey PN. Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants. Proteomics 2017; 18:e1700038. [PMID: 28759167 DOI: 10.1002/pmic.201700038] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/26/2017] [Indexed: 12/18/2022]
Abstract
Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics. We also examine the evidence for new peptides arising from sORFs and discuss their functions in plant development, environmental responses, and translational control.
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Affiliation(s)
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University, Durham, NC, USA
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28
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Hubé F, Ulveling D, Sureau A, Forveille S, Francastel C. Short intron-derived ncRNAs. Nucleic Acids Res 2017; 45:4768-4781. [PMID: 28053119 PMCID: PMC5416886 DOI: 10.1093/nar/gkw1341] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/21/2016] [Indexed: 01/02/2023] Open
Abstract
Introns represent almost half of the human genome, although they are eliminated from transcripts through RNA splicing. Yet, different classes of non-canonical miRNAs have been proposed to originate directly from intron splicing. Here, we considered the alternative splicing of introns as an interesting source of miRNAs, compatible with a developmental switch. We report computational prediction of new Short Intron-Derived ncRNAs (SID), defined as precursors of smaller ncRNAs like miRNAs and snoRNAs produced directly by splicing, and tested their dependence on each key factor in canonical or alternative miRNAs biogenesis (Drosha, DGCR8, DBR1, snRNP70, U2AF65, PRP8, Dicer, Ago2). We found that about half of predicted SID rely on debranching of the excised intron-lariat by the enzyme DBR1, as proposed for mirtrons. However, we identified new classes of SID for which miRNAs biogenesis may rely on intermingling between canonical and alternative pathways. We validated selected SID as putative miRNAs precursors and identified new endogenous miRNAs produced by non-canonical pathways, including one hosted in the first intron of SRA (Steroid Receptor RNA activator). Consistent with increased SRA intron retention during myogenic differentiation, release of SRA intron and its associated mature miRNA decreased in cells from healthy subjects but not from myotonic dystrophy patients with splicing defects.
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Affiliation(s)
- Florent Hubé
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, CNRS UMR 7216, Paris, France
| | - Damien Ulveling
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, CNRS UMR 7216, Paris, France
| | - Alain Sureau
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, CNRS UMR 7216, Paris, France
| | - Sabrina Forveille
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, CNRS UMR 7216, Paris, France
| | - Claire Francastel
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Epigénétique et Destin Cellulaire, CNRS UMR 7216, Paris, France
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Wang H, Wang Y, Xie S, Liu Y, Xie Z. Global and cell-type specific properties of lincRNAs with ribosome occupancy. Nucleic Acids Res 2017; 45:2786-2796. [PMID: 27738133 PMCID: PMC5389576 DOI: 10.1093/nar/gkw909] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/10/2016] [Indexed: 12/17/2022] Open
Abstract
Advances in transcriptomics have led to the discovery of a large number of long intergenic non-coding RNAs (lincRNAs), which are now recognized as important regulators of diverse cellular processes. Although originally thought to be non-coding, recent studies have revealed that many lincRNAs are bound by ribosomes, with a few lincRNAs even having ability to generate micropeptides. The question arises: how widespread the translation of lincRNAs may be and whether such translation is likely to be functional. To better understand biological relevance of lincRNA translation, we systematically characterized lincRNAs with ribosome occupancy by the expression, structural, sequence, evolutionary and functional features for eight human cell lines, revealed that lincRNAs with ribosome occupancy have remarkably distinctive properties compared with those without ribosome occupancy, indicating that translation has important biological implication in categorizing and annotating lincRNAs. Further analysis revealed lincRNAs exhibit remarkable cell-type specificity with differential translational repertoires and substantial discordance in functionality. Collectively, our analyses provide the first attempt to characterize global and cell-type specific properties of translation of lincRNAs in human cells, highlighting that translation of lincRNAs has clear molecular, evolutionary and functional implications. This study will facilitate better understanding of the diverse functions of lincRNAs.
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Affiliation(s)
- Hongwei Wang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yan Wang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shangqian Xie
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Lab of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Center for Precision Medicine, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
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Ramat A, Hannaford M, Januschke J. Maintenance of Miranda Localization in Drosophila Neuroblasts Involves Interaction with the Cognate mRNA. Curr Biol 2017; 27:2101-2111.e5. [PMID: 28690114 PMCID: PMC5526833 DOI: 10.1016/j.cub.2017.06.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/01/2017] [Accepted: 06/07/2017] [Indexed: 11/28/2022]
Abstract
How cells position their proteins is a key problem in cell biology. Targeting mRNAs to distinct regions of the cytoplasm contributes to protein localization by providing local control over translation. Here, we reveal that an interdependence of a protein and cognate mRNA maintains asymmetric protein distribution in mitotic Drosophila neural stem cells. We tagged endogenous mRNA or protein products of the gene miranda that is required for fate determination with GFP. We find that the mRNA localizes like the protein it encodes in a basal crescent in mitosis. We then used GFP-specific nanobodies fused to localization domains to alter the subcellular distribution of the GFP-tagged mRNA or protein. Altering the localization of the mRNA resulted in mislocalization of the protein and vice versa. Protein localization defects caused by mislocalization of the cognate mRNA were rescued by introducing untagged mRNA coding for mutant non-localizable protein. Therefore, by combining the MS2 system and subcellular nanobody expression, we uncovered that maintenance of Mira asymmetric localization requires interaction with the cognate mRNA.
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Affiliation(s)
- Anne Ramat
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, DD5 1EH Dundee, UK
| | - Matthew Hannaford
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, DD5 1EH Dundee, UK
| | - Jens Januschke
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, DD5 1EH Dundee, UK.
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31
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Skalska L, Beltran-Nebot M, Ule J, Jenner RG. Regulatory feedback from nascent RNA to chromatin and transcription. Nat Rev Mol Cell Biol 2017; 18:331-337. [PMID: 28270684 DOI: 10.1038/nrm.2017.12] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transcription and chromatin function are regulated by proteins that bind to DNA, nucleosomes or RNA polymerase II, with specific non-coding RNAs (ncRNAs) functioning to modulate their recruitment or activity. Unlike ncRNAs, nascent pre-mRNA was considered to be primarily a passive player in these processes. In this Opinion article, we describe recently identified interactions between nascent pre-mRNAs and regulatory proteins, highlight commonalities between the functions of nascent pre-mRNA and nascent ncRNA, and propose that both types of RNA have an active role in transcription and chromatin regulation.
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Affiliation(s)
- Lenka Skalska
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Manuel Beltran-Nebot
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Jernej Ule
- Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; and The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard G Jenner
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
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Neuhaus K, Landstorfer R, Simon S, Schober S, Wright PR, Smith C, Backofen R, Wecko R, Keim DA, Scherer S. Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP. BMC Genomics 2017; 18:216. [PMID: 28245801 PMCID: PMC5331693 DOI: 10.1186/s12864-017-3586-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 02/13/2017] [Indexed: 12/14/2022] Open
Abstract
Background While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA. Results Based on their low RCV, 150 novel non-translated EHEC transcripts were identified as putative ncRNAs, representing both antisense and intergenic transcripts, 74 of which had expressed homologs in E. coli MG1655. Bioinformatics analysis predicted statistically significant target regulons for 15 of the intergenic transcripts; experimental analysis revealed 4-fold or higher differential expression of 46 novel ncRNA in different growth media. Out of 329 annotated EHEC ncRNAs, 52 showed an RCV similar to protein-coding genes, of those, 16 had RIBOseq patterns matching annotated genes in other enterobacteriaceae, and 11 seem to possess a Shine-Dalgarno sequence, suggesting that such ncRNAs may encode small proteins instead of being solely non-coding. To support that the RIBOseq signals are reflecting translation, we tested the ribosomal-footprint covered ORF of ryhB and found a phenotype for the encoded peptide in iron-limiting condition. Conclusion Determination of the RCV is a useful approach for a rapid first-step differentiation between bacterial ncRNAs and small mRNAs. Further, many known ncRNAs may encode proteins as well. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3586-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Klaus Neuhaus
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany. .,Core Facility Microbiome/NGS, ZIEL Institute for Food & Health, Weihenstephaner Berg 3, D-85354, Freising, Germany.
| | - Richard Landstorfer
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany
| | - Svenja Simon
- Informatik und Informationswissenschaft, Universität Konstanz, D-78457, Konstanz, Germany
| | - Steffen Schober
- Institut für Nachrichtentechnik, Universität Ulm, Albert-Einstein-Allee 43, D-89081, Ulm, Germany
| | - Patrick R Wright
- Bioinformatics Group, Department of Computer Science and BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, University of Freiburg, D-79110, Freiburg, Germany
| | - Cameron Smith
- Bioinformatics Group, Department of Computer Science and BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, University of Freiburg, D-79110, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science and BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, University of Freiburg, D-79110, Freiburg, Germany
| | - Romy Wecko
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany
| | - Daniel A Keim
- Informatik und Informationswissenschaft, Universität Konstanz, D-78457, Konstanz, Germany
| | - Siegfried Scherer
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, Germany
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33
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Integrative classification of human coding and noncoding genes through RNA metabolism profiles. Nat Struct Mol Biol 2016; 24:86-96. [PMID: 27870833 DOI: 10.1038/nsmb.3325] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/18/2016] [Indexed: 12/26/2022]
Abstract
Pervasive transcription of the human genome results in a heterogeneous mix of coding RNAs and long noncoding RNAs (lncRNAs). Only a small fraction of lncRNAs have demonstrated regulatory functions, thus making functional lncRNAs difficult to distinguish from nonfunctional transcriptional byproducts. This difficulty has resulted in numerous competing human lncRNA classifications that are complicated by a steady increase in the number of annotated lncRNAs. To address these challenges, we quantitatively examined transcription, splicing, degradation, localization and translation for coding and noncoding human genes. We observed that annotated lncRNAs had lower synthesis and higher degradation rates than mRNAs and discovered mechanistic differences explaining slower lncRNA splicing. We grouped genes into classes with similar RNA metabolism profiles, containing both mRNAs and lncRNAs to varying extents. These classes exhibited distinct RNA metabolism, different evolutionary patterns and differential sensitivity to cellular RNA-regulatory pathways. Our classification provides an alternative to genomic context-driven annotations of lncRNAs.
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Abstract
Every ribonucleic acid begins its cellular life as a transcript. If the transcript or its processing product has a function it should be regarded an RNA. Nonfunctional transcripts, by-products from processing, degradation intermediates, even those originating from (functional) RNAs, and non-functional products of transcriptional gene regulation accomplished via the act of transcription, as well as stochastic (co)transcripts could simply be addressed as transcripts (class 0). The copious functional RNAs (class I), often maturing after one or more processing steps, already are systematized into ever expanding sub-classifications ranging from micro RNAs to rRNAs. Established sub-classifications addressing a wide functional diversity remain unaffected. mRNAs (class II) are distinct from any other RNA by virtue of their potential to be translated into (poly)peptide(s) on ribosomes. We are not proposing a novel RNA classification, but wish to add a basic concept with existing terminology (transcript, RNA, and mRNA) that should serve as an additional framework for carefully delineating RNA function from an avalanche of RNA sequencing data. At the same time, this top level hierarchical model should illuminate important principles of RNA evolution and biology thus heightening our awareness that in biology boundaries and categorizations are typically fuzzy.
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Affiliation(s)
- Jürgen Brosius
- a Institute of Experimental Pathology, ZMBE, University of Münster , Von-Esmarch-Str. 56, 48149 ; Münster , Germany.,b Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB) , Fehrbelliner Str. 38, 16816 ; Germany
| | - Carsten A Raabe
- a Institute of Experimental Pathology, ZMBE, University of Münster , Von-Esmarch-Str. 56, 48149 ; Münster , Germany.,b Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB) , Fehrbelliner Str. 38, 16816 ; Germany
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35
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Ulveling D, Le Clerc S, Cobat A, Labib T, Noirel J, Laville V, Coulonges C, Carpentier W, Nalpas B, Heim MH, Poynard T, Cerny A, Pol S, Bochud PY, Dabis F, Theodorou I, Lévy Y, Salmon D, Abel L, Dominguez S, Zagury JF. A new 3p25 locus is associated with liver fibrosis progression in human immunodeficiency virus/hepatitis C virus-coinfected patients. Hepatology 2016; 64:1462-1472. [PMID: 27339598 DOI: 10.1002/hep.28695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/24/2016] [Accepted: 06/11/2016] [Indexed: 12/11/2022]
Abstract
UNLABELLED There is growing evidence that human genetic variants contribute to liver fibrosis in subjects with hepatitis C virus (HCV) monoinfection, but this aspect has been little investigated in patients coinfected with HCV and human immunodeficiency virus (HIV). We performed the first genome-wide association study of liver fibrosis progression in patients coinfected with HCV and HIV, using the well-characterized French National Agency for Research on AIDS and Viral Hepatitis CO13 HEPAVIH cohort. Liver fibrosis was assessed by elastography (FibroScan), providing a quantitative fibrosis score. After quality control, a genome-wide association study was conducted on 289 Caucasian patients, for a total of 8,426,597 genotyped (Illumina Omni2.5 BeadChip) or reliably imputed single-nucleotide polymorphisms. Single-nucleotide polymorphisms with P values <10-6 were investigated in two independent replication cohorts of European patients infected with HCV alone. Two signals of genome-wide significance (P < 5 × 10-8 ) were obtained. The first, on chromosome 3p25 and corresponding to rs61183828 (P = 3.8 × 10-9 ), was replicated in the two independent cohorts of patients with HCV monoinfection. The cluster of single-nucleotide polymorphisms in linkage disequilibrium with rs61183828 was located close to two genes involved in mechanisms affecting both cell signaling and cell structure (CAV3) or HCV replication (RAD18). The second signal, obtained with rs11790131 (P = 9.3 × 10-9 ) on chromosome region 9p22, was not replicated. CONCLUSION This genome-wide association study identified a new locus associated with liver fibrosis severity in patients with HIV/HCV coinfection, on chromosome 3p25, a finding that was replicated in patients with HCV monoinfection; these results provide new relevant hypotheses for the pathogenesis of liver fibrosis in patients with HIV/HCV coinfection that may help define new targets for drug development or new prognostic tests, to improve patient care. (Hepatology 2016;64:1462-1472).
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Affiliation(s)
- Damien Ulveling
- Équipe Génomique, Bioinformatique et Applications (EA4627), Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Sigrid Le Clerc
- Équipe Génomique, Bioinformatique et Applications (EA4627), Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Taoufik Labib
- Équipe Génomique, Bioinformatique et Applications (EA4627), Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Josselin Noirel
- Équipe Génomique, Bioinformatique et Applications (EA4627), Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Vincent Laville
- Équipe Génomique, Bioinformatique et Applications (EA4627), Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Cédric Coulonges
- Équipe Génomique, Bioinformatique et Applications (EA4627), Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France
| | - Wassila Carpentier
- Plateforme Post-Génomique P3S, AP-HP, UPMC Université Paris 6, Faculté de Médecine Pitié Salpétrière, Paris, France
| | - Bertrand Nalpas
- Département d'Hépatologie, Hôpital Cochin (AP-HP), Université Paris Descartes, Paris, France
| | - Markus H Heim
- Department of Gastroenterology, University Hospital, Basel, Switzerland
| | - Thierry Poynard
- Université Pierre et Marie Curie, Service d'Hépato-gastroentérologie, Hôpital Pitié-Salpêtrière (AP-HP), Paris, France
| | | | - Stanislas Pol
- Département d'Hépatologie, Hôpital Cochin (AP-HP), Université Paris Descartes, Paris, France.,INSERM UMS20, Institut Pasteur, Paris, France
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - François Dabis
- Centre de Recherche INSERM U897, Epidemiologie-Biostatistique, Institut de Santé Publique, Epidémiologie et Développement, Université de Bordeaux, Bordeaux, France
| | - Ioannis Theodorou
- Laboratory of Immunity and Infection, Centre d'Immunologie et des Maladies Infectieuses de Paris (CIMI), INSERM U1135, Hôpital Pitié-Salpêtrière (AP-HP), Paris, France.,Plateforme Génomique INSERM-ANRS, Groupe Hospitalier Pitié Salpétrière, AP-HP, UPMC Université Paris 6, Paris, France
| | - Yves Lévy
- INSERM U955, AP-HP, Groupe Henri-Mondor Albert-Chenevier, Immunologie Clinique, Créteil, France
| | - Dominique Salmon
- Department of Infectious Diseases, Cochin Hospital, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Stéphanie Dominguez
- INSERM U955, AP-HP, Groupe Henri-Mondor Albert-Chenevier, Immunologie Clinique, Créteil, France.
| | - Jean-François Zagury
- Équipe Génomique, Bioinformatique et Applications (EA4627), Chaire de Bioinformatique, Conservatoire National des Arts et Métiers, Paris, France.
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Sampath K, Ephrussi A. CncRNAs: RNAs with both coding and non-coding roles in development. Development 2016; 143:1234-41. [PMID: 27095489 DOI: 10.1242/dev.133298] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNAs are known to regulate diverse biological processes, either as protein-encoding molecules or as non-coding RNAs. However, a third class that comprises RNAs endowed with both protein coding and non-coding functions has recently emerged. Such bi-functional 'coding and non-coding RNAs' (cncRNAs) have been shown to play important roles in distinct developmental processes in plants and animals. Here, we discuss key examples of cncRNAs and review their roles, regulation and mechanisms of action during development.
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Affiliation(s)
- Karuna Sampath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AJ, UK
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
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37
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Nitsche A, Stadler PF. Evolutionary clues in lncRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27436689 DOI: 10.1002/wrna.1376] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 12/13/2022]
Abstract
The diversity of long non-coding RNAs (lncRNAs) in the human transcriptome is in stark contrast to the sparse exploration of their functions concomitant with their conservation and evolution. The pervasive transcription of the largely non-coding human genome makes the evolutionary age and conservation patterns of lncRNAs to a topic of interest. Yet it is a fairly unexplored field and not that easy to determine as for protein-coding genes. Although there are a few experimentally studied cases, which are conserved at the sequence level, most lncRNAs exhibit weak or untraceable primary sequence conservation. Recent studies shed light on the interspecies conservation of secondary structures among lncRNA homologs by using diverse computational methods. This highlights the importance of structure on functionality of lncRNAs as opposed to the poor impact of primary sequence changes. Further clues in the evolution of lncRNAs are given by selective constraints on non-coding gene structures (e.g., promoters or splice sites) as well as the conservation of prevalent spatio-temporal expression patterns. However, a rapid evolutionary turnover is observable throughout the heterogeneous group of lncRNAs. This still gives rise to questions about its functional meaning. WIREs RNA 2017, 8:e1376. doi: 10.1002/wrna.1376 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Anne Nitsche
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Institute de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Cedex, France
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany.,Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.,Department of Theoretical Chemistry, University of Vienna, Wien, Austria.,Santa Fe Institute, Santa Fe, NM, USA
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38
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de Andres-Pablo A, Morillon A, Wery M. LncRNAs, lost in translation or licence to regulate? Curr Genet 2016; 63:29-33. [DOI: 10.1007/s00294-016-0615-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 11/28/2022]
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Abstract
Long non-coding RNAs (lncRNAs) are a diverse class of RNAs that engage in numerous biological processes across every branch of life. Although initially discovered as mRNA-like transcripts that do not encode proteins, recent studies have revealed features of lncRNAs that further distinguish them from mRNAs. In this Review, we describe special events in the lifetimes of lncRNAs - before, during and after transcription - and discuss how these events ultimately shape the unique characteristics and functional roles of lncRNAs.
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Affiliation(s)
- Jeffrey J Quinn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305, USA
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Zou Y, Li C, Shu F, Tian Z, Xu W, Xu H, Tian H, Shi R, Mao X. lncRNA expression signatures in periodontitis revealed by microarray: the potential role of lncRNAs in periodontitis pathogenesis. J Cell Biochem 2016; 116:640-7. [PMID: 25399840 DOI: 10.1002/jcb.25015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 11/06/2014] [Indexed: 12/13/2022]
Abstract
Periodontitis, a common chronic inflammatory disease of the periodontium, is caused by dental plaque formation induced by microorganisms. Recent studies have demonstrated that lncRNAs play a critical role in the regulation of gene expression and in the pathogenesis of diseases. To demonstrate that periodontitis is associated with lncRNAs, microarray analysis was used to detect differently expressed lncRNAs in chronic periodontitis and adjacent normal tissues. The results of some differently expressed lncRNAs were further confirmed using real-time PCR. A total of 8925 differentially expressed lncRNAs were detected, including 4313 upregulated lncRNAs and 4612 downregulated lncRNAs. Further lncRNA subgroup analysis showed there were 589 enhancer-like lncRNAs, 238 homeobox (HOX) cluster lncRNAs, and 1218 Rinn's lincRNAs, of which 656 lincRNAs were upregulated and 562 lincRNAs were downregulated. Therefore, we confirmed that lncRNAs were differently expressed in chronic periodontitis tissues compared with adjacent normal tissues, indicating that lncRNAs may exert partial or key roles in periodontitis pathogenesis and development. Taken together, this study may provide potential targets for future treatment of periodontitis and novel diagnostic biomarkers for periodontitis.
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Affiliation(s)
- Yaguang Zou
- Department of Stomatology, NanFang Hospital, Southern Medical University, Guangzhou, 510515, China
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Popa A, Lebrigand K, Barbry P, Waldmann R. Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells. BMC Genomics 2016; 17:52. [PMID: 26764022 PMCID: PMC4712605 DOI: 10.1186/s12864-016-2384-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/06/2016] [Indexed: 01/02/2023] Open
Abstract
Background Open reading frames are common in long noncoding RNAs (lncRNAs) and 5’UTRs of protein coding transcripts (uORFs). The question of whether those ORFs are translated was recently addressed by several groups using ribosome profiling. Most of those studies concluded that certain lncRNAs and uORFs are translated, essentially based on computational analysis of ribosome footprints. However, major discrepancies remain on the scope of translation and the translational status of individual ORFs. In consequence, further criteria are required to reliably identify translated ORFs from ribosome profiling data. Results We examined the effect of the translation inhibitors pateamine A, harringtonine and puromycin on murine ES cell ribosome footprints. We found that pateamine A, a drug that targets eIF4A, allows a far more accurate identification of translated sequences than previously used drugs and computational scoring schemes. Our data show that at least one third but less than two thirds of ES cell lncRNAs are translated. We also identified translated uORFs in hundreds of annotated coding transcripts including key pluripotency transcripts, such as dicer, lin28, trim71, and ctcf. Conclusion Pateamine A inhibition data clearly increase the precision of the detection of translated ORFs in ribosome profiling experiments. Our data show that translation of lncRNAs and uORFs in murine ES cells is rather common although less pervasive than previously suggested. The observation of translated uORFs in several key pluripotency transcripts suggests that translational regulation by uORFs might be part of the network that defines mammalian stem cell identity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2384-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra Popa
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), University Nice Sophia Antipolis, CNRS, F06560, Sophia-Antipolis, France
| | - Kevin Lebrigand
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), University Nice Sophia Antipolis, CNRS, F06560, Sophia-Antipolis, France
| | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), University Nice Sophia Antipolis, CNRS, F06560, Sophia-Antipolis, France.
| | - Rainer Waldmann
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), University Nice Sophia Antipolis, CNRS, F06560, Sophia-Antipolis, France
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Long Noncoding RNAs as New Architects in Cancer Epigenetics, Prognostic Biomarkers, and Potential Therapeutic Targets. BIOMED RESEARCH INTERNATIONAL 2015; 2015:320214. [PMID: 26448935 PMCID: PMC4584070 DOI: 10.1155/2015/320214] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 05/06/2015] [Indexed: 12/27/2022]
Abstract
Recent advances in genome-wide analysis have revealed that 66% of the genome is actively transcribed into noncoding RNAs (ncRNAs) while less than 2% of the sequences encode proteins. Among ncRNAs, high-resolution microarray and massively parallel sequencing technologies have identified long ncRNAs (>200 nucleotides) that lack coding protein function. LncRNAs abundance, nuclear location, and diversity allow them to create in association with protein interactome, a complex regulatory network orchestrating cellular phenotypic plasticity via modulation of all levels of protein-coding gene expression. Whereas lncRNAs biological functions and mechanisms of action are still not fully understood, accumulating data suggest that lncRNAs deregulation is pivotal in cancer initiation and progression and metastatic spread through various mechanisms, including epigenetic effectors, alternative splicing, and microRNA-like molecules. Mounting data suggest that several lncRNAs expression profiles in malignant tumors are associated with prognosis and they can be detected in biological fluids. In this review, we will briefly discuss characteristics and functions of lncRNAs, their role in carcinogenesis, and their potential usefulness as diagnosis and prognosis biomarkers and novel therapeutic targets.
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Khandelwal A, Bacolla A, Vasquez KM, Jain A. Long non-coding RNA: A new paradigm for lung cancer. Mol Carcinog 2015; 54:1235-51. [PMID: 26332907 DOI: 10.1002/mc.22362] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/05/2015] [Accepted: 06/26/2015] [Indexed: 12/14/2022]
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Recent advances in whole genome transcriptome analysis have enabled the identification of numerous members of a novel class of non-coding RNAs, i.e., long non-coding RNAs (lncRNAs), which play important roles in a wide range of biological processes and whose deregulation causes human disease, including cancer. Herein we provide a comprehensive survey of lncRNAs associated with lung cancer, with particular focus on the functions that either facilitate or inhibit the progression of lung cancer and the pathways involved. Emerging data on the use of lncRNAs as biomarkers for the diagnosis and prognosis of cancer are also discussed. We cast this information within the wider perspective of lncRNA biogenesis and molecular functions in the cell. Relationships that exist between lncRNAs, genome-wide transcription, and lung cancer are discussed. Deepening our understanding on these processes is critical not only from a mechanistic standpoint, but also for the development of novel biomarkers and effective therapeutic targets for cancer patients.
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Affiliation(s)
- Akanksha Khandelwal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India
| | - Albino Bacolla
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, University of Texas, Austin, Texas
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, University of Texas, Austin, Texas
| | - Aklank Jain
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India
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Hubé F, Francastel C. "Pocket-sized RNA-Seq": A Method to Capture New Mature microRNA Produced from a Genomic Region of Interest. Noncoding RNA 2015; 1:127-138. [PMID: 29861419 PMCID: PMC5932543 DOI: 10.3390/ncrna1020127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/03/2015] [Accepted: 06/23/2015] [Indexed: 12/28/2022] Open
Abstract
Currently, the discovery of new small ncRNAs requires high throughput methods even in the case of focused research on the regulation of specific genes or set of genes. We propose herein a simple, rapid, efficient, and cost effective method to clone and sequence single, yet unknown, small ncRNA. This technique that we called “Pocket-sized RNA-Seq” or psRNA-seq is based on in vitro transcription, RNA pull down and adapted RACE-PCR methods that allow its implementation using either available commercial kits or in-house reagents.
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Affiliation(s)
- Florent Hubé
- University Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France.
- Epigénétique et Destin Cellulaire, CNRS UMR 7216, 75013 Paris, France.
| | - Claire Francastel
- University Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France.
- Epigénétique et Destin Cellulaire, CNRS UMR 7216, 75013 Paris, France.
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45
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Panzeri I, Rossetti G, Abrignani S, Pagani M. Long Intergenic Non-Coding RNAs: Novel Drivers of Human Lymphocyte Differentiation. Front Immunol 2015; 6:175. [PMID: 25926836 PMCID: PMC4397839 DOI: 10.3389/fimmu.2015.00175] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/28/2015] [Indexed: 12/29/2022] Open
Abstract
Upon recognition of a foreign antigen, CD4(+) naïve T lymphocytes proliferate and differentiate into subsets with distinct functions. This process is fundamental for the effective immune system function, as CD4(+) T cells orchestrate both the innate and adaptive immune response. Traditionally, this differentiation event has been regarded as the acquisition of an irreversible cell fate so that memory and effector CD4(+) T subsets were considered terminally differentiated cells or lineages. Consequently, these lineages are conventionally defined thanks to their prototypical set of cytokines and transcription factors. However, recent findings suggest that CD4(+) T lymphocytes possess a remarkable phenotypic plasticity, as they can often re-direct their functional program depending on the milieu they encounter. Therefore, new questions are now compelling such as which are the molecular determinants underlying plasticity and stability and how the balance between these two opposite forces drives the cell fate. As already mentioned, in some cases, the mere expression of cytokines and master regulators could not fully explain lymphocytes plasticity. We should consider other layers of regulation, including epigenetic factors such as the modulation of chromatin state or the transcription of non-coding RNAs, whose high cell-specificity give a hint on their involvement in cell fate determination. In this review, we will focus on the recent advances in understanding CD4(+) T lymphocytes subsets specification from an epigenetic point of view. In particular, we will emphasize the emerging importance of non-coding RNAs as key players in these differentiation events. We will also present here new data from our laboratory highlighting the contribution of long non-coding RNAs in driving human CD4(+) T lymphocytes differentiation.
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Affiliation(s)
- Ilaria Panzeri
- Integrative Biology Unit, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", IRCCS Ospedale Maggiore Policlinico , Milano , Italy
| | - Grazisa Rossetti
- Integrative Biology Unit, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", IRCCS Ospedale Maggiore Policlinico , Milano , Italy
| | - Sergio Abrignani
- Integrative Biology Unit, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", IRCCS Ospedale Maggiore Policlinico , Milano , Italy
| | - Massimiliano Pagani
- Integrative Biology Unit, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", IRCCS Ospedale Maggiore Policlinico , Milano , Italy ; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano , Milano , Italy
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Nagano H, Yamagishi N, Tomida C, Yano C, Aibara K, Kohno S, Abe T, Ohno A, Hirasaka K, Okumura Y, Mills EM, Nikawa T, Teshima-Kondo S. A novel myogenic function residing in the 5' non-coding region of Insulin receptor substrate-1 (Irs-1) transcript. BMC Cell Biol 2015; 16:8. [PMID: 25887310 PMCID: PMC4373113 DOI: 10.1186/s12860-015-0054-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/16/2015] [Indexed: 11/20/2022] Open
Abstract
Background There is evidence that several messenger RNAs (mRNAs) are bifunctional RNAs, i.e. RNA transcript carrying both protein-coding capacity and activity as functional non-coding RNA via 5′ and 3′ untranslated regions (UTRs). Results In this study, we identified a novel bifunctional RNA that is transcribed from insulin receptor substrate-1 (Irs-1) gene with full-length 5′UTR sequence (FL-Irs-1 mRNA). FL-Irs-1 mRNA was highly expressed only in skeletal muscle tissue. In cultured skeletal muscle C2C12 cells, the FL-Irs-1 transcript functioned as a bifunctional mRNA. The FL-Irs-1 transcript produced IRS-1 protein during differentiation of myoblasts into myotubes; however, this transcript functioned as a regulatory RNA in proliferating myoblasts. The FL-Irs-1 5′UTR contains a partial complementary sequence to Rb mRNA, which is a critical factor for myogenic differentiation. The overexpression of the 5′UTR markedly reduced Rb mRNA expression, and this reduction was fully dependent on the complementary element and was not compensated by IRS-1 protein. Conversely, knockdown of FL-Irs-1 mRNA increased Rb mRNA expression and enhanced myoblast differentiation into myotubes. Conclusions Our findings suggest that the FL-Irs-1 transcript regulates myogenic differentiation as a regulatory RNA in myoblasts. Electronic supplementary material The online version of this article (doi:10.1186/s12860-015-0054-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hikaru Nagano
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan. .,Facalty of Nutritional Science, Sagami Women's University, Sagamihara, 252-0383, Japan.
| | - Naoko Yamagishi
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Chisato Tomida
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Chiaki Yano
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Kana Aibara
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Shohei Kohno
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Tomoki Abe
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Ayako Ohno
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Katsuya Hirasaka
- Graduate school of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, 852-8521, Japan.
| | - Yuushi Okumura
- Facalty of Nutritional Science, Sagami Women's University, Sagamihara, 252-0383, Japan.
| | - Edward M Mills
- Division of Pharmacology/Toxicology, College of Pharmacy, University of Texas at Austin, Austin, Texas.
| | - Takeshi Nikawa
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Shigetada Teshima-Kondo
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
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Mammalian introns: when the junk generates molecular diversity. Int J Mol Sci 2015; 16:4429-52. [PMID: 25710723 PMCID: PMC4394429 DOI: 10.3390/ijms16034429] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 01/14/2023] Open
Abstract
Introns represent almost half of the human genome, yet their vast majority is eliminated from eukaryotic transcripts through RNA splicing. Nevertheless, they feature key elements and functions that deserve further interest. At the level of DNA, introns are genomic segments that can shelter independent transcription units for coding and non-coding RNAs which transcription may interfere with that of the host gene, and regulatory elements that can influence gene expression and splicing itself. From the RNA perspective, some introns can be subjected to alternative splicing. Intron retention appear to provide some plasticity to the nature of the protein produced, its distribution in a given cell type and timing of its translation. Intron retention may also serve as a switch to produce coding or non-coding RNAs from the same transcription unit. Conversely, splicing of introns has been directly implicated in the production of small regulatory RNAs. Hence, splicing of introns also appears to provide plasticity to the type of RNA produced from a genetic locus (coding, non-coding, short or long). We addressed these aspects to add to our understanding of mechanisms that control the fate of introns and could be instrumental in regulating genomic output and hence cell fate.
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de Boer FK, Hogeweg P. Mutation rates and evolution of multiple coding in RNA-based protocells. J Mol Evol 2014; 79:193-203. [PMID: 25280530 PMCID: PMC4247474 DOI: 10.1007/s00239-014-9648-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 09/18/2014] [Indexed: 11/28/2022]
Abstract
RNA has a myriad of biological roles in contemporary life. We use the RNA paradigm for genotype-phenotype mappings to study the evolution of multiple coding in dependence to mutation rates. We study three different one-to-many genotype-phenotype mappings which have the potential to encode the information for multiple functions on a single sequence. These three different maps are (i) cofolding, where two sequences can bind and “cofold,” (ii) suboptimal folding, where the alternative foldings within a certain range of the native state of sequences are considered, and (iii) adapter-based folding, in which protocells can evolve adapter-mediated alternative foldings. We study how protocells with a set of sequences can code for a set of predefined functional structures, while avoiding all other structures, which are considered to be misfoldings. Note that such misfolded structures are far more prevalent than functional ones. Our results highlight the flexibility of the RNA sequence to secondary structure mapping and the power of evolution to shape the genotype-phenotype mapping. We show that high fitness can be achieved even at high mutation rates. Mutation rates affect genome size, but differently depending on which folding method is used. We observe that cofolding limits the possibility to avoid misfolded structures and that adapters are always beneficial for fitness, but even more beneficial at low mutation rates. In all cases, the evolution procedure selects for molecules that can form additional structures. Our results indicate that inherent properties of RNA molecules and their interactions allow the evolution of complexity even at high mutation rates.
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Affiliation(s)
- Folkert K de Boer
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Utrecht, The Netherlands,
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LncRBase: an enriched resource for lncRNA information. PLoS One 2014; 9:e108010. [PMID: 25233092 PMCID: PMC4169474 DOI: 10.1371/journal.pone.0108010] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/11/2014] [Indexed: 11/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are noncoding transcripts longer than 200 nucleotides, which show evidence of pervasive transcription and participate in a plethora of cellular regulatory processes. Although several noncoding transcripts have been functionally annotated as lncRNAs within the genome, not all have been proven to fulfill the criteria for a functional regulator and further analyses have to be done in order to include them in a functional cohort. LncRNAs are being classified and reclassified in an ongoing annotation process, and the challenge is fraught with ambiguity, as newer evidences of their biogenesis and functional implication come into light. In our effort to understand the complexity of this still enigmatic biomolecule, we have developed a new database entitled "LncRBase" where we have classified and characterized lncRNAs in human and mouse. It is an extensive resource of human and mouse lncRNA transcripts belonging to fourteen distinct subtypes, with a total of 83,201 entries for mouse and 133,361 entries for human: among these, we have newly annotated 8,507 mouse and 14,813 human non coding RNA transcripts (from UCSC and H-InvDB 8.0) as lncRNAs. We have especially considered protein coding gene loci which act as hosts for non coding transcripts. LncRBase includes different lncRNA transcript variants of protein coding genes within LncRBase. LncRBase provides information about the genomic context of different lncRNA subtypes, their interaction with small non coding RNAs (ncRNAs) viz. piwi interacting RNAs (piRNAs) and microRNAs (miRNAs) and their mode of regulation, via association with diverse other genomic elements. Adequate knowledge about genomic origin and molecular features of lncRNAs is essential to understand their functional and behavioral complexities. Overall, LncRBase provides a thorough study on various aspects of lncRNA origin and function and a user-friendly interface to search for lncRNA information. LncRBase is available at http://bicresources.jcbose.ac.in/zhumur/lncrbase.
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50
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Ulveling D, Dinger ME, Francastel C, Hubé F. Identification of a dinucleotide signature that discriminates coding from non-coding long RNAs. Front Genet 2014; 5:316. [PMID: 25250049 PMCID: PMC4158813 DOI: 10.3389/fgene.2014.00316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/22/2014] [Indexed: 11/13/2022] Open
Abstract
To date, the main criterion by which long ncRNAs (lncRNAs) are discriminated from mRNAs is based on the capacity of the transcripts to encode a protein. However, it becomes important to identify non-ORF-based sequence characteristics that can be used to parse between ncRNAs and mRNAs. In this study, we first established an extremely selective workflow to define a highly refined database of lncRNAs which was used for comparison with mRNAs. Then using this highly selective collection of lncRNAs, we found the CG dinucleotide frequencies were clearly distinct. In addition, we showed that the bias in CG dinucleotide frequency was conserved in human and mouse genomes. We propose that this sequence feature will serve as a useful classifier in transcript classification pipelines. We also suggest that our refined database of "bona fide" lncRNAs will be valuable for the discovery of other sequence characteristics distinct to lncRNAs.
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Affiliation(s)
- Damien Ulveling
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - Marcel E Dinger
- The University of Queensland Diamantina Institute, The University of Queensland Brisbane, QLD, Australia
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - Florent Hubé
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité Paris, France
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