1
|
Lai T, Yu Q, Pan J, Wang J, Tang Z, Bai X, Shi L, Zhou T. The Identification and Comparative Analysis of Non-Coding RNAs in Spores and Mycelia of Penicillium expansum. J Fungi (Basel) 2023; 9:999. [PMID: 37888255 PMCID: PMC10607695 DOI: 10.3390/jof9100999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Penicillium expansum is the most popular post-harvest pathogen and causes blue mold disease in pome fruit and leads to significant economic losses worldwide every year. However, the fundamental regulation mechanisms of growth in P. expansum are unclear. Recently, non-coding RNAs (ncRNAs) have attracted more attention due to critical roles in normalizing gene expression and maintaining cellular genotypes in organisms. However, the research related to ncRNAs in P. expansum have not been reported. Therefore, to provide an overview of ncRNAs on composition, distribution, expression changes, and potential targets in the growth process, a comparative transcriptomic analysis was performed on spores and mycelia of P. expansum in the present study. A total of 2595 novel mRNAs, 3362 long non-coding RNAs (lncRNAs), 10 novel microRNAs (miRNAs), 86 novel small interfering RNAs (siRNAs), and 11,238 circular RNAs (circRNAs) were predicted and quantified. Of these, 1482 novel mRNAs, 5987 known mRNAs, 2047 lncRNAs, 40 miRNAs, 38 novel siRNAs, and 9235 circRNAs were differentially expressed (DE) in response to the different development stages. Afterward, the involved functions and pathways of DE RNAs were revealed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database enrichment analysis. The interaction networks between mRNAs, lncRNAs, and miRNAs were also predicted based on their correlation coefficient of expression profiles. Among them, it was found that miR168 family members may play important roles in fungal growth due to their central location in the network. These findings will contribute to a better understanding on regulation machinery at the RNA level on fungal growth and provide a theoretical basis to develop novel control strategies against P. expansum.
Collapse
Affiliation(s)
- Tongfei Lai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Qinru Yu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Jingjing Pan
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Jingjing Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Zhenxing Tang
- School of Culinary Arts, Tourism College of Zhejiang, Hangzhou 311231, China;
| | - Xuelian Bai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Lue Shi
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| | - Ting Zhou
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (T.L.); (Q.Y.); (J.P.); (J.W.); (X.B.); (L.S.)
| |
Collapse
|
2
|
Lelandais G, Remy D, Malagnac F, Grognet P. New insights into genome annotation in Podospora anserina through re-exploiting multiple RNA-seq data. BMC Genomics 2022; 23:859. [PMID: 36581831 PMCID: PMC9801653 DOI: 10.1186/s12864-022-09085-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Publicly available RNA-seq datasets are often underused although being helpful to improve functional annotation of eukaryotic genomes. This is especially true for filamentous fungi genomes which structure differs from most well annotated yeast genomes. Podospora anserina is a filamentous fungal model, which genome has been sequenced and annotated in 2008. Still, the current annotation lacks information about cis-regulatory elements, including promoters, transcription starting sites and terminators, which are instrumental to integrate epigenomic features into global gene regulation strategies. RESULTS Here we took advantage of 37 RNA-seq experiments that were obtained in contrasted developmental and physiological conditions, to complete the functional annotation of P. anserina genome. Out of the 10,800 previously annotated genes, 5'UTR and 3'UTR were defined for 7554, among which, 3328 showed differential transcriptional signal starts and/or transcriptional end sites. In addition, alternative splicing events were detected for 2350 genes, mostly due alternative 3'splice sites and 1732 novel transcriptionally active regions (nTARs) in unannotated regions were identified. CONCLUSIONS Our study provides a comprehensive genome-wide functional annotation of P. anserina genome, including chromatin features, cis-acting elements such as UTRs, alternative splicing events and transcription of non-coding regions. These new findings will likely improve our understanding of gene regulation strategies in compact genomes, such as those of filamentous fungi. Characterization of alternative transcripts and nTARs paves the way to the discovery of putative new genes, alternative peptides or regulatory non-coding RNAs.
Collapse
Affiliation(s)
- Gaëlle Lelandais
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Damien Remy
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Fabienne Malagnac
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pierre Grognet
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| |
Collapse
|
3
|
Navigating the Multiverse of Antisense RNAs: The Transcription- and RNA-Dependent Dimension. Noncoding RNA 2022; 8:ncrna8060074. [PMID: 36412909 PMCID: PMC9680235 DOI: 10.3390/ncrna8060074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022] Open
Abstract
Evidence accumulated over the past decades shows that the number of identified antisense transcripts is continuously increasing, promoting them from transcriptional noise to real genes with specific functions. Indeed, recent studies have begun to unravel the complexity of the antisense RNA (asRNA) world, starting from the multidimensional mechanisms that they can exert in physiological and pathological conditions. In this review, we discuss the multiverse of the molecular functions of asRNAs, describing their action through transcription-dependent and RNA-dependent mechanisms. Then, we report the workflow and methodologies to study and functionally characterize single asRNA candidates.
Collapse
|
4
|
Choi G, Jeon J, Lee H, Zhou S, Lee YH. Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection. BMC Genomics 2022; 23:132. [PMID: 35168559 PMCID: PMC8845233 DOI: 10.1186/s12864-022-08380-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/09/2022] [Indexed: 12/05/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) play essential roles in developmental processes and disease development at the transcriptional and post-transcriptional levels across diverse taxa. However, only few studies have profiled fungal lncRNAs in a genome-wide manner during host infection. Results Infection-associated lncRNAs were identified using lncRNA profiling over six stages of host infection (e.g., vegetative growth, pre-penetration, biotrophic, and necrotrophic stages) in the model pathogenic fungus, Magnaporthe oryzae. We identified 2,601 novel lncRNAs, including 1,286 antisense lncRNAs and 980 intergenic lncRNAs. Among the identified lncRNAs, 755 were expressed in a stage-specific manner and 560 were infection-specifically expressed lncRNAs (ISELs). To decipher the potential roles of lncRNAs during infection, we identified 365 protein-coding genes that were associated with 214 ISELs. Analysis of the predicted functions of these associated genes suggested that lncRNAs regulate pathogenesis-related genes, including xylanases and effectors. Conclusions The ISELs and their associated genes provide a comprehensive view of lncRNAs during fungal pathogen-plant interactions. This study expands new insights into the role of lncRNAs in the rice blast fungus, as well as other plant pathogenic fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08380-4.
Collapse
Affiliation(s)
- Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea.,Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea.,Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Hyunjun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Shenxian Zhou
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea. .,Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea. .,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea. .,Center for Plant Microbiome Research, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
| |
Collapse
|
5
|
Wang J, Zeng W, Cheng J, Xie J, Fu Y, Jiang D, Lin Y. lncRsp1, a long noncoding RNA, influences Fgsp1 expression and sexual reproduction in Fusarium graminearum. MOLECULAR PLANT PATHOLOGY 2022; 23:265-277. [PMID: 34841640 PMCID: PMC8743023 DOI: 10.1111/mpp.13160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/05/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Long noncoding RNAs (lncRNAs) are crucial regulators of gene expression in many biological processes, but their biological functions remain largely unknown, especially in fungi. Fusarium graminearum is an important pathogen that causes the destructive disease Fusarium head blight (FHB) or head scab disease on wheat and barley. In our previous RNA sequencing (RNA-Seq) study, we discovered that lncRsp1 is an lncRNA that is located +99 bp upstream of a putative sugar transporter gene, Fgsp1, with the same transcription direction. Functional studies revealed that ΔlncRsp1 and ΔFgsp1 were normal in growth and conidiation but had defects in ascospore discharge and virulence on wheat coleoptiles. Moreover, lncRsp1 and Fgsp1 were shown to negatively regulate the expression of several deoxynivalenol (DON) biosynthesis genes, TRI4, TRI5, TRI6, and TRI13, as well as DON production. Further analysis showed that the overexpression of lncRsp1 enhanced the ability of ascospore release and increased the mRNA expression level of the Fgsp1 gene, while lncRsp1-silenced strains reduced ascospore discharge and inhibited Fgsp1 expression during the sexual reproduction stage. In addition, the lncRsp1 complementary strains lncRsp1-LC-1 and lncRsp1-LC-2 restored ascospore discharge to the level of the wild-type strain PH-1. Taken together, our results reveal the distinct and specific functions of lncRsp1 and Fgsp1 in F. graminearum and principally demonstrate that lncRsp1 can affect the release of ascospores by regulating the expression of Fgsp1.
Collapse
Affiliation(s)
- Jie Wang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Wenping Zeng
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Environment Change and Resources Use in Beibu GulfMinistry of EducationNanning Normal UniversityNanningChina
| | - Jiasen Cheng
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Jiatao Xie
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Yanping Fu
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Daohong Jiang
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| | - Yang Lin
- Hubei Key Laboratory of Plant PathologyHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
6
|
Liu N, Wang P, Li X, Pei Y, Sun Y, Ma X, Ge X, Zhu Y, Li F, Hou Y. Long Non-Coding RNAs profiling in pathogenesis of Verticillium dahliae: New insights in the host-pathogen interaction. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 314:111098. [PMID: 34895536 DOI: 10.1016/j.plantsci.2021.111098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/29/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
Verticillium dahliae causes vascular wilt disease on cotton (Gossypium hirsutum), resulting in devastating yield loss worldwide. While little is known about the mechanism of long non-coding RNAs (lncRNAs), several lncRNAs have been implicated in numerous physiological processes and diseases. To better understand V. dahliae pathogenesis, lncRNA was conducted in a V. dahliae virulence model. Potential target genes of significantly regulated lncRNAs were predicted using cis/trans-regulatory algorithms. This study provides evidence for lncRNAs' regulatory role in pathogenesis-related genes. Interestingly, lncRNAs were identified and varying in terms of RNA length and nutrient starvation treatments. Efficient pathogen nutrition during the interaction with the host is a requisite factor during infection. Our observations directly link to mutated V. dahliae invasion, explaining infected cotton have lower pathogenicity and lethality compared to V. dahliae. Remarkably, lncRNAs XLOC_006536 and XLOC_000836 involved in the complex regulation of pathogenesis-related genes in V. dahliae were identified. For the first time the regulatory role of lncRNAs in filamentous fungi was uncovered, and it is our contention that elucidation of lncRNAs will advance our understanding in the development and pathogenesis of V. dahliae and offer alternatives in the control of the diseases caused by fungus V. dahliae attack.
Collapse
Affiliation(s)
- Nana Liu
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Ping Wang
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Xiancai Li
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Yakun Pei
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Yun Sun
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Xiaowen Ma
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, People's Republic of China
| | - Yutao Zhu
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, People's Republic of China.
| | - Yuxia Hou
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China.
| |
Collapse
|
7
|
Ranjbar R, Behjatfar M, Teimouri A, Aghaie Fard A, Maniati M, Taheri-Anganeh M. Long non-coding RNAs and microorganism-associated cancers. Cell Biochem Funct 2021; 39:844-853. [PMID: 34227160 DOI: 10.1002/cbf.3657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 06/25/2021] [Indexed: 12/26/2022]
Abstract
Cancerous cells are abnormal cells characterized by aberrant growth and proliferation, which can involve various types of cells and tissues. Through numerous signalling pathways, many mechanisms are involved in cells that keep them normal. These signalling pathways are tightly set by different proteins whose expression is regulated by a large number of factors. In other words, when a regulating factor does not act properly or undergoes a change in its function or expression, the result will be that the subordinate gene and subsequently the related protein will show deranged expression and activity. This leads to disordered signalling pathways which bring about uncontrolled proliferation in cells. One of the most significant factors in adjusting the expression of genes is noncoding RNAs. It should be noted that all underlying causes initiating malignancy try to alter the main regulatory factors in cellular processes and gene expression and direct the cell to an unregulated state. Microorganisms have been identified as one of the important elements to direct normal cells to abnormality. That is, they probably agitate the malignant traits through manipulating significant factors such as ncRNAs in given cells using their own or host-related factors. The present study is aimed at examining how the long noncoding RNAs are involved in microorganism-mediated cancers.
Collapse
Affiliation(s)
- Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mojtaba Behjatfar
- Department of Electrical Engineering, Kazeroon Branch, Islamic Azad University, Kazeroon, Iran
| | - Ali Teimouri
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arad Aghaie Fard
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahmood Maniati
- English Department, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mortaza Taheri-Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
8
|
Tang J, Chen X, Yan Y, Huang J, Luo C, Tom H, Zheng L. Comprehensive transcriptome profiling reveals abundant long non-coding RNAs associated with development of the rice false smut fungus, Ustilaginoidea virens. Environ Microbiol 2021; 23:4998-5013. [PMID: 33587785 DOI: 10.1111/1462-2920.15432] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 02/10/2021] [Indexed: 12/28/2022]
Abstract
Long non-coding RNAs (lncRNAs) play an important role in biological processes but regulation and function of lncRNAs remain largely unelucidated, especially in fungi. Ustilaginoidea virens is an economically important fungus causing a devastating disease of rice. By combining microscopic and RNA-seq analyses, we comprehensively characterized lncRNAs of this fungus in infection and developmental processes and defined four serial typical stages. RNA-seq analyses revealed 1724 lncRNAs in U. virens, including 1084 long intergenic non-coding RNAs (lincRNAs), 51 intronic RNAs (incRNAs), 566 natural antisense transcripts (lncNATs) and 23 sense transcripts. Gene Ontology enrichment of differentially expressed lincRNAs and lncNATs demonstrated that these were mainly involved in transport-related regulation. Functional studies of transport-related lncRNAs revealed that UvlncNAT-MFS, a cytoplasm localized lncNAT of a putative MFS transporter gene, UvMFS, could form an RNA duplex with UvMFS and was required for regulation of growth, conidiation and various stress responses. Our results were the first to elucidate the lncRNA profiles during infection and development of this important phytopathogen U. virens. The functional discovery of the novel lncRNA, UvlncNAT-MFS, revealed the potential of lncRNAs in regulation of life processes in fungi.
Collapse
Affiliation(s)
- Jintian Tang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China.,Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Xiaoyang Chen
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yaqin Yan
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junbin Huang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaoxi Luo
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hsiang Tom
- School of Environmental Sciences, University of Guelph, Guelph, N1G 2W1, Canada
| | - Lu Zheng
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
9
|
Wang J, Zeng W, Xie J, Fu Y, Jiang D, Lin Y, Chen W, Cheng J. A novel antisense long non-coding RNA participates in asexual and sexual reproduction by regulating the expression of GzmetE in Fusarium graminearum. Environ Microbiol 2021; 23:4939-4955. [PMID: 33438341 DOI: 10.1111/1462-2920.15399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 01/09/2021] [Indexed: 11/27/2022]
Abstract
Fusarium graminearum is an important worldwide pathogen that causes Fusarium head blight in wheat, barley, maize and other grains. LncRNAs play important roles in many biological processes, but little is known about their functions and mechanisms in filamentous fungi. Here, we report that a natural antisense RNA, GzmetE-AS, is transcribed from the opposite strand of GzmetE. GzmetE encodes a homoserine O-acetyltransferase, which is important for sexual development and plant infection. The expression of GzmetE-AS was increased significantly during the conidiation stage, while GzmetE was upregulated in the late stage of sexual reproduction. Overexpression of GzmetE-AS inhibited the transcription of GzmetE. In contrast, the expression of GzmetE was significantly increased in GzmetE-AS transcription termination strain GzmetE-AS-T. Furthermore, GzmetE-AS-T produced more perithecia and facilitated the ascospore discharge, resembling the phenotype of GzmetE overexpressing strains. However, overexpression of GzmetE-AS in ∆dcl1/2 strain cannot inhibit the expression of GzmetE, and the GzmetE nat-siRNA is also significantly reduced in ∆dcl1/2 mutant. Taken together, we have identified a novel antisense lncRNA GzmetE-AS, which is involved in asexual and sexual reproduction by regulating its antisense gene GzmetE through RNAi pathway. Our findings reveal that the lncRNA plays critical roles in the development of F. graminearum.
Collapse
Affiliation(s)
- Jie Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenping Zeng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, 530001, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Lin
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weidong Chen
- United States Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, WA, 99164, USA
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
10
|
Parra-Rivero O, Pardo-Medina J, Gutiérrez G, Limón MC, Avalos J. A novel lncRNA as a positive regulator of carotenoid biosynthesis in Fusarium. Sci Rep 2020; 10:678. [PMID: 31959816 PMCID: PMC6971296 DOI: 10.1038/s41598-020-57529-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/07/2019] [Indexed: 01/28/2023] Open
Abstract
The fungi Fusarium oxysporum and Fusarium fujikuroi produce carotenoids, lipophilic terpenoid pigments of biotechnological interest, with xanthophyll neurosporaxanthin as the main end product. Their carotenoid biosynthesis is activated by light and negatively regulated by the RING-finger protein CarS. Global transcriptomic analysis identified in both species a putative 1-kb lncRNA that we call carP, referred to as Fo-carP and Ff-carP in each species, upstream to the gene carS and transcribed from the same DNA strand. Fo-carP and Ff-carP are poorly transcribed, but their RNA levels increase in carS mutants. The deletion of Fo-carP or Ff-carP in the respective species results in albino phenotypes, with strong reductions in mRNA levels of structural genes for carotenoid biosynthesis and higher mRNA content of the carS gene, which could explain the low accumulation of carotenoids. Upon alignment, Fo-carP and Ff-carP show 75-80% identity, with short insertions or deletions resulting in a lack of coincident ORFs. Moreover, none of the ORFs found in their sequences have indications of possible coding functions. We conclude that Fo-carP and Ff-carP are regulatory lncRNAs necessary for the active expression of the carotenoid genes in Fusarium through an unknown molecular mechanism, probably related to the control of carS function or expression.
Collapse
Affiliation(s)
- Obdulia Parra-Rivero
- Department of Genetics, Faculty of Biology, University of Seville, E-41012, Seville, Spain
| | - Javier Pardo-Medina
- Department of Genetics, Faculty of Biology, University of Seville, E-41012, Seville, Spain
| | - Gabriel Gutiérrez
- Department of Genetics, Faculty of Biology, University of Seville, E-41012, Seville, Spain
| | - M Carmen Limón
- Department of Genetics, Faculty of Biology, University of Seville, E-41012, Seville, Spain
| | - Javier Avalos
- Department of Genetics, Faculty of Biology, University of Seville, E-41012, Seville, Spain.
| |
Collapse
|
11
|
Wang Z, Jiang Y, Wu H, Xie X, Huang B. Genome-Wide Identification and Functional Prediction of Long Non-coding RNAs Involved in the Heat Stress Response in Metarhizium robertsii. Front Microbiol 2019; 10:2336. [PMID: 31649657 PMCID: PMC6794563 DOI: 10.3389/fmicb.2019.02336] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play a significant role in stress responses. To date, only a few studies have reported the role of lncRNAs in insect-pathogenic fungi. Here, we report a genome-wide transcriptional analysis of lncRNAs produced in response to heat stress in Metarhizium robertsii, a model insect-pathogenic fungus, using strand-specific RNA sequencing. A total of 1655 lncRNAs with 1742 isoforms were identified, of which 1081 differentially expressed (DE) lncRNAs were characterized as being heat responsive. By characterizing their genomic structures and expression patterns, we found that the lncRNAs possessed shorter transcripts, fewer exons, and lower expression levels than the protein-coding genes in M. robertsii. Furthermore, target prediction analysis of the lncRNAs revealed thousands of potential DE lncRNA–messenger RNA (mRNA) pairs, among which 5381 pairs function in the cis-regulatory mode. Further pathway enrichment analysis of the corresponding cis-regulated target genes showed that the targets were significantly enriched in the following biological pathways: the Hippo signaling pathway and cell cycle. This finding suggested that these DE lncRNAs control the expression of their corresponding neighboring genes primarily through environmental information processing and cellular processes. Moreover, only 26 trans-regulated lncRNA–mRNA pairs were determined. In addition, among the targets of heat-responsive lncRNAs, two classic genes that may be involved in the response to heat stress were also identified, including hsp70 (XM_007821830 and XM_007825705). These findings expand our knowledge of lncRNAs as important regulators of the response to heat stress in filamentous fungi, including M. robertsii.
Collapse
Affiliation(s)
- Zhangxun Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China.,School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yuanyuan Jiang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China.,School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Hao Wu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Xiangyun Xie
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| |
Collapse
|
12
|
Yang H, Wang X, Li Z, Guo Q, Yang M, Chen D, Wang C. The Effect of Blue Light on the Production of Citrinin in Monascus purpureus M9 by Regulating the mraox Gene through lncRNA AOANCR. Toxins (Basel) 2019; 11:toxins11090536. [PMID: 31540336 PMCID: PMC6784174 DOI: 10.3390/toxins11090536] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 02/06/2023] Open
Abstract
Blue light, as an important environmental factor, can regulate the production of various secondary metabolites of Monascus purpureus M9, including mycotoxin-citrinin, pigments, and monacolin K. The analysis of citrinin in Monascus M9 exposed to blue light for 0 min./d, 15 min./d, and 60 min./d showed that 15 min./d of blue light illumination could significantly increase citrinin production, while 60 min./d of blue light illumination decreased citrinin production. Analysis of long non-coding RNA (LncRNA) was performed on the transcripts of Monascus M9 under three culture conditions, and this analysis identified an lncRNA named AOANCR that can negatively regulate the mraox gene. Fermentation studies suggested that alternate respiratory pathways could be among the pathways that are involved in the regulation of the synthesis of citrinin by environmental factors. Aminophylline and citric acid were added to the culture medium to simulate the process of generating cyclic adenosine monophosphate (cAMP) in cells under illumination conditions. The results of the fermentation showed that aminophylline and citric acid could increase the expression of the mraox gene, decrease the expression of lncRNA AOANCR, and reduce the yield of citrinin. This result also indicates a reverse regulation relationship between lncRNA AOANCR and the mraox gene. A blue light signal might regulate the mraox gene at least partially through lncRNA AOANCR, thereby regulating citrinin production. Citrinin has severe nephrotoxicity in mammals, and it is important to control the residual amout of citrinin in red yeast products during fermentation. LncRNA AOANCR and mraox can potentially be used as new targets for the control of citrinin production.
Collapse
Affiliation(s)
- Hua Yang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Xufeng Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Zhenjing Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Qingbin Guo
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Mingguan Yang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Di Chen
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China.
| | - Changlu Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| |
Collapse
|
13
|
Zhu Q, Ramakrishnan M, Park J, Belden WJ. Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci. BMC Genomics 2019; 20:350. [PMID: 31068130 PMCID: PMC6505117 DOI: 10.1186/s12864-019-5729-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/24/2019] [Indexed: 01/01/2023] Open
Abstract
Background Histone H3 lysine 4 tri-methylation (H3K4me3) and histone H3 lysine 9 tri-methylation (H3K9me3) are widely perceived to be opposing and often mutually exclusive chromatin modifications. However, both are needed for certain light-activated genes in Neurospora crassa (Neurospora), including frequency (frq) and vivid (vvd). Except for these 2 loci, little is known about how H3K4me3 and H3K9me3 impact and contribute to light-regulated gene expression. Results In this report, we performed a multi-dimensional genomic analysis to understand the role of H3K4me3 and H3K9me3 using the Neurospora light response as the system. RNA-seq on strains lacking H3 lysine 4 methyltransferase (KMT2/SET-1) and histone H3 lysine 9 methyltransferase (KMT1/DIM-5) revealed some light-activated genes had altered expression, but the light response was largely intact. Comparing these 2 mutants to wild-type (WT), we found that roughly equal numbers of genes showed elevated and reduced expression in the dark and the light making the environmental stimulus somewhat ancillary to the genome-wide effects. ChIP-seq experiments revealed H3K4me3 and H3K9me3 had only minor changes in response to light in WT, but there were notable alterations in H3K4me3 in Δkmt1/Δdim-5 and H3K9me3 in Δkmt2/Δset-1 indicating crosstalk and redistribution between the modifications. Integrated analysis of the RNA-seq and ChIP-seq highlighted context-dependent roles for KMT2/SET1 and KMT1/DIM-5 as either co-activators or co-repressors with some overlap as co-regulators. At a small subset of loci, H3K4 methylation is required for H3K9me3-mediated facultative heterochromatin including, the central clock gene frequency (frq). Finally, we used sequential ChIP (re-ChIP) experiment to confirm Neurospora contains K4/K9 bivalent domains. Conclusions Collectively, these data indicate there are obfuscated regulatory roles for H3K4 methylation and H3K9 methylation depending on genome location with some minor overlap and co-dependency. Electronic supplementary material The online version of this article (10.1186/s12864-019-5729-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Qiaoqiao Zhu
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Mukund Ramakrishnan
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.,Current Address: Department of Biological Sciences, IISER Berhampur, Berhampur, Ganjam, Odisha, 760010, India
| | - Jinhee Park
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - William J Belden
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| |
Collapse
|
14
|
Distribution, Characteristics, and Regulatory Potential of Long Noncoding RNAs in Brown-Rot Fungi. Int J Genomics 2019; 2019:9702342. [PMID: 31192251 PMCID: PMC6525899 DOI: 10.1155/2019/9702342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/07/2019] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNAs have been thoroughly studied in plants, animals, and yeasts, where they play important roles as regulators of transcription. Nevertheless, almost nothing is known about their presence and characteristics in filamentous fungi, especially in basidiomycetes. In the present study, we have carried out an exhaustive annotation and characterization of lncRNAs in two lignin degrader basidiomycetes, Coniophora puteana and Serpula lacrymans. We identified 2,712 putative lncRNAs in the former and 2,242 in the latter, mainly originating from intergenic locations of transposon-sparse genomic regions. The lncRNA length, GC content, expression levels, and stability of the secondary structure differ from coding transcripts but are similar in these two species and resemble that of other eukaryotes. Nevertheless, they lack sequence conservation. Also, we found that lncRNAs are transcriptionally regulated in the same proportion as genes when the fungus actively decomposes soil organic matter. Finally, up to 7% of the upstream gene regions of Coniophora puteana and Serpula lacrymans are transcribed and produce lncRNAs. The study of expression trends in these gene-lncRNA pairs uncovered groups with similar and opposite transcriptional profiles which may be the result of cis-transcriptional regulation.
Collapse
|
15
|
Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts. Fungal Genet Biol 2018; 121:1-9. [PMID: 30223087 DOI: 10.1016/j.fgb.2018.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 12/16/2022]
Abstract
Early-diverging anaerobic fungi (order: Neocallimastigomycota), lignocelluolytic chytrid-like fungi central to fiber degradation in the digestive tracts of large herbivores, are attractive sources of cellulases and hemicellulases for biotechnology. Enzyme expression is tightly regulated and coordinated through mechanisms that remain unelucidated to optimize hydrolytic efficiency. Our analysis of anaerobic fungal transcriptomes reveals hundreds of cis-natural antisense transcripts (cis-NATs), which we hypothesize play an integral role in this regulation. Through integrated genomic and transcriptomic sequencing on a range of catabolic substrates, we validate these NATs in three species (Anaeromyces robustus, Neocallimasix californiae, and Piromyces finnis), and analyze their expression patterns and prevalence to gain insight into their function. NAT function was diverse and conserved across the three fungal genomes studied, with 10% of all metabolic process NATs associated with lignocellulose hydrolysis. Despite these similarities, however, only eleven gene targets were conserved orthologs. Several NATs were dynamically regulated by lignocellulosic substrates while their gene targets were unregulated. This observation is consistent with a hypothesized, but untested, regulatory mechanism where selected genes are exclusively regulated at the transcriptional/post-transcriptional level by NATs. However, only genes with high NAT relative expression levels displayed this phenomenon, suggesting a selection mechanism that favors larger dynamic ranges for more precise control of gene expression. In addition to this mode, we observed two other possible regulatory fates: canonical transcriptional regulation with no NAT response, and positive co-regulation of target mRNA and cognate NAT, which we hypothesize is a fine-tuning strategy to locally negate control outputs from global regulators. Our work reveals the complex contributions of antisense RNA to the catabolic response in anaerobic fungi, highlighting its importance in understanding lignocellulolytic activity for bioenergy applications. More importantly, the relative expression of NAT to target may form a critical determinant of transcriptional vs post-transcriptional (NAT) control of gene expression in primitive anaerobic fungi.
Collapse
|
16
|
Hu Q, Lin X, Ding L, Zeng Y, Pang D, Ouyang N, Xiang Y, Yao H. ARHGAP42 promotes cell migration and invasion involving PI3K/Akt signaling pathway in nasopharyngeal carcinoma. Cancer Med 2018; 7:3862-3874. [PMID: 29936709 PMCID: PMC6089169 DOI: 10.1002/cam4.1552] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 02/26/2018] [Accepted: 04/05/2018] [Indexed: 12/20/2022] Open
Abstract
Rho GTPase-activating protein 42 was identified as an inhibitor of RhoA to maintain normal blood pressure homeostasis. However, the effect of ARHGAP42 in promoting cell malignancy in nasopharyngeal carcinoma is demonstrated in this study. Microarray and real-time quantitative PCR were used for a mRNA profiling of ARHGAP42 in nasopharyngeal primary and metastatic carcinoma tissues. Western blot and immunohistochemical staining were used for detecting the expression of ARHGAP42 protein in nasopharyngeal carcinoma tissues and cell lines. The overexpression and silence experiments of ARHGAP42 were performed in NPC cell lines using siRNA and expressive plasmid for evaluating cancer cell migration and invasion in vitro. Real-time quantitative PCR, western blot, and transwell test were employed for with the function of ARHGAP42 and its antisense lncRNA uc010rul. We confirmed the elevated expression of ARHGAP42 in metastatic NPC tissues of mRNA and protein for the first time. Immunohistochemical analysis indicated that NPC patients with highly ARHGAP42 expression were significantly associated with shorter metastasis-free survival. Knockdown of ARHGAP42 resulted in significant inhibition of nasopharyngeal cancer cell migration and invasion in vitro, and the overexpression of ARHGAP42 showed the opposite effects. In addition, the silence of uc010rul resulted in ARHGAP42 expression decrease and significant inhibition of nasopharyngeal cancer cell migration and invasion. High expression of ARHGAP42 is associated with poor metastasis-free survival of nasopharyngeal carcinoma patients. ARHGAP42 promotes migration and invasion of nasopharyngeal carcinoma cells in vitro; the antisense lncRNA may be involved in this effect.
Collapse
Affiliation(s)
- Qian Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital of Sun Yat‐Sen UniversityGuangzhouChina
- Department of OncologySun Yat‐Sen University Cancer CenterGuangzhouChina
- Department of Breast Cancer OncologyFoshan Hospital of Sun Yat‐Sen UniversityFoshanChina
| | - Xiao Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital of Sun Yat‐Sen UniversityGuangzhouChina
- Department of Breast Cancer OncologySun Yat‐Sen Memorial Hospital of Sun Yat‐Sen UniversityGuangzhouChina
| | - Linxiaoxiao Ding
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital of Sun Yat‐Sen UniversityGuangzhouChina
- Department of Breast Cancer OncologySun Yat‐Sen Memorial Hospital of Sun Yat‐Sen UniversityGuangzhouChina
| | - Yinduo Zeng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital of Sun Yat‐Sen UniversityGuangzhouChina
- Department of Breast Cancer OncologySun Yat‐Sen Memorial Hospital of Sun Yat‐Sen UniversityGuangzhouChina
| | - Danmei Pang
- Department of Breast Cancer OncologyFoshan Hospital of Sun Yat‐Sen UniversityFoshanChina
| | - Nengtai Ouyang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital of Sun Yat‐Sen UniversityGuangzhouChina
| | - Yanqun Xiang
- Department of Nasopharyngeal CarcinomaSun Yat‐Sen University Cancer CenterGuangzhouChina
| | - Herui Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationSun Yat‐Sen Memorial Hospital of Sun Yat‐Sen UniversityGuangzhouChina
- Department of Breast Cancer OncologySun Yat‐Sen Memorial Hospital of Sun Yat‐Sen UniversityGuangzhouChina
| |
Collapse
|
17
|
Guo R, Chen D, Xiong C, Hou C, Zheng Y, Fu Z, Diao Q, Zhang L, Wang H, Hou Z, Li W, Kumar D, Liang Q. Identification of long non-coding RNAs in the chalkbrood disease pathogen Ascospheara apis. J Invertebr Pathol 2018; 156:1-5. [PMID: 29894727 DOI: 10.1016/j.jip.2018.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 01/14/2023]
Abstract
Ascospheara apis is a widespread fungal pathogen that exclusively invades honeybee larvae. Thus far, non-coding RNA in A. apis has not yet been documented. In this study, we sequenced A. apis using strand specific cDNA library construction and Illumina RNA sequencing methods, and identified 379 lncRNAs, including antisense lncRNAs, lincRNAs, intronic lncRNAs and sense lncRNAs. Additionally, these lncRNAs were found to be shorter in length and have fewer exons and transcript isoforms than protein-coding genes, similar to those identified in mammals and plants. Furthermore, the existence of 15 predicted lncRNAs of A. apis was confirmed using RT-PCR and expression levels of 11 were lower than those of adjacent protein-coding genes. Our findings not only enlarge the lncRNA database for fungi, but also lay a foundation for further investigation of potential lncRNA-mediated regulation of genes in A. apis.
Collapse
Affiliation(s)
- Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Cuiling Xiong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Yanzhen Zheng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongmin Fu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Lu Zhang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongquan Wang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhixian Hou
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wendong Li
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dhiraj Kumar
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Qin Liang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
18
|
Cemel IA, Ha N, Schermann G, Yonekawa S, Brunner M. The coding and noncoding transcriptome of Neurospora crassa. BMC Genomics 2017; 18:978. [PMID: 29258423 PMCID: PMC5738166 DOI: 10.1186/s12864-017-4360-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/29/2017] [Indexed: 12/17/2022] Open
Abstract
Background Long non protein coding RNAs (lncRNAs) have been identified in many different organisms and cell types. Emerging examples emphasize the biological importance of these RNA species but their regulation and functions remain poorly understood. In the filamentous fungus Neurospora crassa, the annotation and characterization of lncRNAs is incomplete. Results We have performed a comprehensive transcriptome analysis of Neurospora crassa by using ChIP-seq, RNA-seq and polysome fractionation datasets. We have annotated and characterized 1478 long intergenic noncoding RNAs (lincRNAs) and 1056 natural antisense transcripts, indicating that 20% of the RNA Polymerase II transcripts of Neurospora are not coding for protein. Both classes of lncRNAs accumulate at lower levels than protein-coding mRNAs and they are considerably shorter. Our analysis showed that the vast majority of lincRNAs and antisense transcripts do not contain introns and carry less H3K4me2 modifications than similarly expressed protein coding genes. In contrast, H3K27me3 modifications inversely correlate with transcription of protein coding and lincRNA genes. We show furthermore most lincRNA sequences evolve rapidly, even between phylogenetically close species. Conclusions Our transcriptome analyses revealed distinct features of Neurospora lincRNAs and antisense transcripts in comparison to mRNAs and showed that the prevalence of noncoding transcripts in this organism is higher than previously anticipated. The study provides a broad repertoire and a resource for further studies of lncRNAs. Electronic supplementary material The online version of this article (10.1186/s12864-017-4360-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ibrahim Avi Cemel
- Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany
| | - Nati Ha
- Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany.,present address: Cellzome GmbH, 69117, Heidelberg, Germany
| | - Geza Schermann
- Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany
| | - Shusuke Yonekawa
- Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany.,present address: Yoshida & Co., Ltd., Tokyo, 151-8580, Japan
| | - Michael Brunner
- Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany.
| |
Collapse
|
19
|
Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
Collapse
Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
| |
Collapse
|
20
|
Knap P, Tebaldi T, Di Leva F, Biagioli M, Dalla Serra M, Viero G. The Unexpected Tuners: Are LncRNAs Regulating Host Translation during Infections? Toxins (Basel) 2017; 9:E357. [PMID: 29469820 PMCID: PMC5705972 DOI: 10.3390/toxins9110357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/27/2022] Open
Abstract
Pathogenic bacteria produce powerful virulent factors, such as pore-forming toxins, that promote their survival and cause serious damage to the host. Host cells reply to membrane stresses and ionic imbalance by modifying gene expression at the epigenetic, transcriptional and translational level, to recover from the toxin attack. The fact that the majority of the human transcriptome encodes for non-coding RNAs (ncRNAs) raises the question: do host cells deploy non-coding transcripts to rapidly control the most energy-consuming process in cells-i.e., host translation-to counteract the infection? Here, we discuss the intriguing possibility that membrane-damaging toxins induce, in the host, the expression of toxin-specific long non-coding RNAs (lncRNAs), which act as sponges for other molecules, encoding small peptides or binding target mRNAs to depress their translation efficiency. Unravelling the function of host-produced lncRNAs upon bacterial infection or membrane damage requires an improved understanding of host lncRNA expression patterns, their association with polysomes and their function during this stress. This field of investigation holds a unique opportunity to reveal unpredicted scenarios and novel approaches to counteract antibiotic-resistant infections.
Collapse
Affiliation(s)
- Primoz Knap
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
| | - Toma Tebaldi
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Francesca Di Leva
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, Povo Trento 38123, Italy.
| | - Marta Biagioli
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, Povo Trento 38123, Italy.
| | - Mauro Dalla Serra
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
| |
Collapse
|
21
|
Shao J, Chen H, Yang D, Jiang M, Zhang H, Wu B, Li J, Yuan L, Liu C. Genome-wide Identification and Characterization of Natural Antisense Transcripts by Strand-specific RNA Sequencing in Ganoderma lucidum. Sci Rep 2017; 7:5711. [PMID: 28720793 PMCID: PMC5515960 DOI: 10.1038/s41598-017-04303-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/12/2017] [Indexed: 12/13/2022] Open
Abstract
Ganoderma lucidum is a white-rot fungus best-known for its medicinal and ligninolytic activities. To discover the underlying genes responsible for these activities, we identified and characterized the natural antisense transcripts (NATs) using strand-specific (ss) RNA-seq data obtained from the mycelia, primordia and fruiting bodies. NATs were identified using a custom pipeline and then subjected to functional enrichment and differential expression analyses. A total of 1613 cis- and 244 trans- sense and antisense transcripts were identified. Mapping to GO terms and KEGG pathways revealed that NATs were frequently associated with genes of particular functional categories in particular stages. ssRT-qPCR experiments showed that the expression profiles of 30 of 50 (60%) transcripts were highly correlated with those of the RNA-seq results (r ≥ 0.9). Expression profiles of 22 of 25 (88%) pairs of NATs and STs were highly correlated (p ≤ 0.01), with 15 having r ≥ 0.8 and 4 having r ≤ -0.8. Six lignin-modifying genes and their NATs were analyzed in detail. Diverse patterns of differential expression among different stages and positive and negative correlations were observed. These results suggested that NATs were implicated in gene expression regulation in a function-group and developmental-stage specific manner through complex mechanisms.
Collapse
Affiliation(s)
- Junjie Shao
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Dan Yang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Hui Zhang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Bin Wu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Jianqin Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Lichai Yuan
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P.R. China.
| |
Collapse
|
22
|
Donaldson ME, Ostrowski LA, Goulet KM, Saville BJ. Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression. BMC Genomics 2017; 18:340. [PMID: 28464849 PMCID: PMC5414199 DOI: 10.1186/s12864-017-3720-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/25/2017] [Indexed: 12/12/2022] Open
Abstract
Background Biotrophic fungal plant pathogens cause billions of dollars in losses to North American crops annually. The model for functional investigation of these fungi is Ustilago maydis. Its 20.5 Mb annotated genome sequence has been an excellent resource for investigating biotrophic plant pathogenesis. Expressed-sequence tag libraries and microarray hybridizations have provided insight regarding the type of transcripts produced by U. maydis but these analyses were not comprehensive and there were insufficient data for transcriptome comparison to other smut fungi. To improve transcriptome annotation and enable comparative analyses, comprehensive strand-specific RNA-seq was performed on cell-types of three related smut species: U. maydis (common smut of corn), Ustilago hordei (covered smut of barley), and Sporisorium reilianum (head smut of corn). Results In total, >1 billion paired-end sequence reads were obtained from haploid cell, dikaryon and teliospore RNA of U. maydis, haploid cell RNA of U. hordei, and haploid and dikaryon cell RNA of S. reilianum. The sequences were assembled into transfrags using Trinity, and updated gene models were created using PASA and categorized with Cufflinks Cuffcompare. Representative genes that were predicted for the first time with these RNA-seq analyses and genes with novel annotation features were independently assessed by reverse transcriptase PCR. The analyses indicate hundreds more predicted proteins, relative to the previous genome annotation, could be produced by U. maydis from altered transcript forms, and that the number of non-coding RNAs produced, including transcribed intergenic sequences and natural antisense transcripts, approximately equals the number of mRNAs. This high representation of non-coding RNAs appears to be a conserved feature of the smut fungi regardless of whether they have RNA interference machinery. Approximately 50% of the identified NATs were conserved among the smut fungi. Conclusions Overall, these analyses revealed: 1) smut genomes encode a number of transcriptional units that is twice the number of annotated protein-coding genes, 2) a small number of intergenic transcripts may encode proteins with characteristics of fungal effectors, 3) the vast majority of intergenic and antisense transcripts do not contain ORFs, 4) a large proportion of the identified antisense transcripts were detected at orthologous loci among the smut fungi, and 5) there is an enrichment of functional categories among orthologous loci that suggests antisense RNAs could have a genome-wide, non-RNAi-mediated, influence on gene expression in smut fungi. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3720-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Michael E Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada
| | - Lauren A Ostrowski
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada.,Present Address: Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Kristi M Goulet
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada
| | - Barry J Saville
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, K9L 0G2, ON, Canada. .,Forensic Science Program, Trent University, Peterborough, K9L 0G2, ON, Canada.
| |
Collapse
|
23
|
Nejat N, Mantri N. Emerging roles of long non-coding RNAs in plant response to biotic and abiotic stresses. Crit Rev Biotechnol 2017; 38:93-105. [PMID: 28423944 DOI: 10.1080/07388551.2017.1312270] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Spectacular progress in high-throughput transcriptome sequencing and expression profiling using next-generation sequencing technologies have recently revolutionized molecular biology and allowed massive advances in identifying the genomic regions and molecular mechanisms underlying transcriptional regulation of growth, development, and stress response. Through recent research, non-coding RNAs, in particular long non-coding RNAs, have emerged as key regulators of transcription in eukaryotes. Long non-coding RNAs are vastly heterogeneous groups of RNAs that execute a broad range of essential roles in various biological processes at the epigenetic, transcriptional, and post-transcriptional levels. They modulate transcription through diverse mechanisms. Recently, numerous lncRNAs have been identified to be associated with defense responses to biotic and abiotic stresses. These have been suggested to perform indispensable roles in plant immunity and adaptation to environmental conditions. However, only a few lncRNAs have been functionally characterized in plants. In this paper, we summarize the present knowledge of lncRNAs, review the recent advances in understanding regulatory functions of lncRNAs, and highlight the emerging roles of lncRNAs in regulating immune responses in plants.
Collapse
Affiliation(s)
- Naghmeh Nejat
- a School of Science, Health Innovations Research Institute, RMIT University , Melbourne , Victoria , Australia
| | - Nitin Mantri
- a School of Science, Health Innovations Research Institute, RMIT University , Melbourne , Victoria , Australia
| |
Collapse
|
24
|
Qi Z, Smith KM, Bredeweg EL, Bosnjak N, Freitag M, Nargang FE. Alternative Oxidase Transcription Factors AOD2 and AOD5 of Neurospora crassa Control the Expression of Genes Involved in Energy Production and Metabolism. G3 (BETHESDA, MD.) 2017; 7:449-466. [PMID: 27986792 PMCID: PMC5295593 DOI: 10.1534/g3.116.035402] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/22/2016] [Indexed: 01/16/2023]
Abstract
In Neurospora crassa, blocking the function of the standard mitochondrial electron transport chain results in the induction of an alternative oxidase (AOX). AOX transfers electrons directly from ubiquinol to molecular oxygen. AOX serves as a model of retrograde regulation since it is encoded by a nuclear gene that is regulated in response to signals from mitochondria. The N. crassa transcription factors AOD2 and AOD5 are necessary for the expression of the AOX gene. To gain insight into the mechanism by which these factors function, and to determine if they have roles in the expression of additional genes in N. crassa, we constructed strains expressing only tagged versions of the proteins. Cell fractionation experiments showed that both proteins are localized to the nucleus under both AOX inducing and noninducing conditions. Furthermore, chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) analysis revealed that the proteins are bound to the promoter region of the AOX gene under both conditions. ChIP-seq also showed that the transcription factors bind to the upstream regions of a number of genes that are involved in energy production and metabolism. Dependence on AOD2 and AOD5 for the expression of several of these genes was verified by quantitative PCR. The majority of ChIP-seq peaks observed were enriched for both AOD2 and AOD5. However, we also observed occasional sites where one factor appeared to bind preferentially. The most striking of these was a conserved sequence that bound large amounts of AOD2 but little AOD5. This sequence was found within a 310 bp repeat unit that occurs at several locations in the genome.
Collapse
Affiliation(s)
- Zhigang Qi
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Kristina M Smith
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003
| | - Erin L Bredeweg
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003
| | - Natasa Bosnjak
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003
| | - Frank E Nargang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| |
Collapse
|
25
|
Strategies to identify natural antisense transcripts. Biochimie 2017; 132:131-151. [DOI: 10.1016/j.biochi.2016.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/24/2016] [Indexed: 12/15/2022]
|
26
|
Dang Y, Cheng J, Sun X, Zhou Z, Liu Y. Antisense transcription licenses nascent transcripts to mediate transcriptional gene silencing. Genes Dev 2016; 30:2417-2432. [PMID: 27856616 PMCID: PMC5131781 DOI: 10.1101/gad.285791.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/21/2016] [Indexed: 12/21/2022]
Abstract
In this study, Dang et al. use Neurospora to demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism. In eukaryotes, antisense transcription can regulate sense transcription by induction of epigenetic modifications. We showed previously that antisense transcription triggers Dicer-independent siRNA (disiRNA) production and disiRNA locus DNA methylation (DLDM) in Neurospora crassa. Here we show that the conserved exonuclease ERI-1 (enhanced RNAi-1) is a critical component in this process. Antisense transcription and ERI-1 binding to target RNAs are necessary and sufficient to trigger DLDM. Convergent transcription causes stalling of RNA polymerase II during transcription, which permits ERI-1 to bind nascent RNAs in the nucleus and recruit a histone methyltransferase complex that catalyzes chromatin modifications. Furthermore, we show that, in the cytoplasm, ERI-1 targets hundreds of transcripts from loci without antisense transcription to regulate RNA stability. Together, our results demonstrate a critical role for transcription kinetics in long noncoding RNA-mediated epigenetic modifications and identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptional RNA metabolism.
Collapse
Affiliation(s)
- Yunkun Dang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xianyun Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, ZhongGuanCun, Beijing 100080, China
| | - Zhipeng Zhou
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| |
Collapse
|
27
|
Li H, Wang Y, Chen M, Xiao P, Hu C, Zeng Z, Wang C, Wang J, Hu Z. Genome-wide long non-coding RNA screening, identification and characterization in a model microorganism Chlamydomonas reinhardtii. Sci Rep 2016; 6:34109. [PMID: 27659799 PMCID: PMC5034253 DOI: 10.1038/srep34109] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/05/2016] [Indexed: 01/20/2023] Open
Abstract
Microalgae are regarded as the most promising biofuel candidates and extensive metabolic engineering were conducted but very few improvements were achieved. Long non-coding RNA (lncRNA) investigation and manipulation may provide new insights for this issue. LncRNAs refer to transcripts that are longer than 200 nucleotides, do not encode proteins but play important roles in eukaryotic gene regulation. However, no information of potential lncRNAs has been reported in eukaryotic alga. Recently, we performed RNA sequencing in Chlamydomonas reinhardtii, and obtained totally 3,574 putative lncRNAs. 1440 were considered as high-confidence lncRNAs, including 936 large intergenic, 310 intronic and 194 anti-sense lncRNAs. The average transcript length, ORF length and numbers of exons for lncRNAs are much less than for genes in this green alga. In contrast with human lncRNAs of which more than 98% are spliced, the percentage in C. reinhardtii is only 48.1%. In addition, we identified 367 lncRNAs responsive to sulfur deprivation, including 36 photosynthesis-related lncRNAs. This is the first time that lncRNAs were explored in the unicellular model organism C. reinhardtii. The lncRNA data could also provide new insights into C. reinhardtii hydrogen production under sulfur deprivation.
Collapse
Affiliation(s)
- Hui Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China.,Shenzhen Key Laboratory of Marine Bioresource &Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China
| | - Yuting Wang
- Shenzhen Key Laboratory of Marine Bioresource &Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, P. R. China
| | - Meirong Chen
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China.,Shenzhen Key Laboratory of Marine Bioresource &Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China
| | - Peng Xiao
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China.,Shenzhen Key Laboratory of Marine Bioresource &Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China
| | - Changxing Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China.,Shenzhen Key Laboratory of Marine Bioresource &Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China
| | - Zhiyong Zeng
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China.,Shenzhen Key Laboratory of Marine Bioresource &Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China
| | - Chaogang Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China.,Shenzhen Key Laboratory of Marine Bioresource &Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China
| | - Jiangxin Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China.,Shenzhen Key Laboratory of Marine Bioresource &Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetic, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China.,Shenzhen Key Laboratory of Marine Bioresource &Eco-environmental Science, College of Life Sciences, Shenzhen University, Shenzhen 518060, P. R. China
| |
Collapse
|
28
|
Joshi RK, Megha S, Basu U, Rahman MH, Kav NNV. Genome Wide Identification and Functional Prediction of Long Non-Coding RNAs Responsive to Sclerotinia sclerotiorum Infection in Brassica napus. PLoS One 2016; 11:e0158784. [PMID: 27388760 PMCID: PMC4936718 DOI: 10.1371/journal.pone.0158784] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/22/2016] [Indexed: 12/03/2022] Open
Abstract
Sclerotinia stem rot caused by Sclerotinia sclerotiorum affects canola production worldwide. Emerging evidence suggests that long non-coding RNAs (lncRNAs) play important roles in the regulation of gene expression in plants, in response to both abiotic and biotic stress. So far, identification of lncRNAs has been limited to a few model plant species, and their roles in mediating responses to biotic stresses are yet to be characterized in Brassica napus. The present study reports the identification of novel lncRNAs responsive to S. sclerotiorum infection in B. napus at two time points after infection (24 hpi and 48 hpi) using a stranded RNA-Sequencing technique and a detection pipeline for lncRNAs. Of the total 3,181 lncRNA candidates, 2,821 lncRNAs were intergenic, 111 were natural antisense transcripts, 76 possessed exonic overlap with the reference coding transcripts while the remaining 173 represented novel lnc- isoforms. Forty one lncRNAs were identified as the precursors for microRNAs (miRNAs) including miR156, miR169 and miR394, with significant roles in mediating plant responses to fungal phytopathogens. A total of 931 differentially expressed lncRNAs were identified in response to S. sclerotiorum infection and the expression of 12 such lncRNAs was further validated using qRT-PCR. B. napus antisense lncRNA, TCONS_00000966, having 90% overlap with a plant defensin gene, showed significant induction at both infection stages, suggesting its involvement in the transcriptional regulation of defense responsive genes under S. sclerotiorum infection. Additionally, nine lncRNAs showed overlap with cis-regulatory regions of differentially expressed genes of B. napus. Quantitative RT-PCR verification of a set of S. sclerotiorum responsive sense/antisense transcript pairs revealed contrasting expression patterns, supporting the hypothesis that steric clashes of transcriptional machinery may lead to inactivation of sense promoter. Our findings highlight the potential contributions of lncRNAs in regulating expression of plant genes that respond to biotic stress.
Collapse
Affiliation(s)
- Raj Kumar Joshi
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
- Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Swati Megha
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Urmila Basu
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Muhammad H. Rahman
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Nat N. V. Kav
- Department of Agricultural Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| |
Collapse
|
29
|
Zhou S, Ding F, Gu X. Non-coding RNAs as Emerging Regulators of Neural Injury Responses and Regeneration. Neurosci Bull 2016; 32:253-64. [PMID: 27037691 DOI: 10.1007/s12264-016-0028-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/14/2016] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a large cluster of RNAs that do not encode proteins, but have multiple functions in diverse cellular processes. Mounting evidence indicates the involvement of ncRNAs in the physiology and pathophysiology of the central and peripheral nervous systems. It has been shown that numerous ncRNAs, especially microRNAs and long non-coding RNAs, are differentially expressed after insults such as acquired brain injury, spinal cord injury, and peripheral nerve injury. These ncRNAs affect neuronal survival, neurite regrowth, and glial phenotype primarily by targeting specific mRNAs, resulting in translation repression or degradation of the mRNAs. An increasing number of studies have investigated the regulatory roles of microRNAs and long non-coding RNAs in neural injury and regeneration, and thus a new research field is emerging. In this review, we highlight current progress in the field in an attempt to provide further insight into post-transcriptional changes occurring after neural injury, and to facilitate the potential use of ncRNAs for improving neural regeneration. We also suggest potential directions for future studies.
Collapse
Affiliation(s)
- Songlin Zhou
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Fei Ding
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Xiaosong Gu
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
| |
Collapse
|
30
|
Chacko N, Zhao Y, Yang E, Wang L, Cai JJ, Lin X. The lncRNA RZE1 Controls Cryptococcal Morphological Transition. PLoS Genet 2015; 11:e1005692. [PMID: 26588844 PMCID: PMC4654512 DOI: 10.1371/journal.pgen.1005692] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 10/30/2015] [Indexed: 02/01/2023] Open
Abstract
In the fungal pathogen Cryptococcus neoformans, the switch from yeast to hypha is an important morphological process preceding the meiotic events during sexual development. Morphotype is also known to be associated with cryptococcal virulence potential. Previous studies identified the regulator Znf2 as a key decision maker for hypha formation and as an anti-virulence factor. By a forward genetic screen, we discovered that a long non-coding RNA (lncRNA) RZE1 functions upstream of ZNF2 in regulating yeast-to-hypha transition. We demonstrate that RZE1 functions primarily in cis and less effectively in trans. Interestingly, RZE1's function is restricted to its native nucleus. Accordingly, RZE1 does not appear to directly affect Znf2 translation or the subcellular localization of Znf2 protein. Transcriptome analysis indicates that the loss of RZE1 reduces the transcript level of ZNF2 and Znf2's prominent downstream targets. In addition, microscopic examination using single molecule fluorescent in situ hybridization (smFISH) indicates that the loss of RZE1 increases the ratio of ZNF2 transcripts in the nucleus versus those in the cytoplasm. Taken together, this lncRNA controls Cryptococcus yeast-to-hypha transition through regulating the key morphogenesis regulator Znf2. This is the first functional characterization of a lncRNA in a human fungal pathogen. Given the potential large number of lncRNAs in the genomes of Cryptococcus and other fungal pathogens, the findings implicate lncRNAs as an additional layer of genetic regulation during fungal development that may well contribute to the complexity in these "simple" eukaryotes.
Collapse
Affiliation(s)
- Nadia Chacko
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Youbao Zhao
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Ence Yang
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Linqi Wang
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - James J. Cai
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Xiaorong Lin
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| |
Collapse
|
31
|
Tao H, Yang JJ, Zhou X, Deng ZY, Shi KH, Li J. Emerging role of long noncoding RNAs in lung cancer: Current status and future prospects. Respir Med 2015; 110:12-9. [PMID: 26603340 DOI: 10.1016/j.rmed.2015.10.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 01/01/2023]
Abstract
Lung cancer is the leading cause of cancer-related death worldwide with a 5-year survival rate of less than 15%, despite significant advances in both diagnostic and therapeutic approaches. Combined genomic and transcriptomic sequencing studies have identified numerous genetic driver mutations that are responsible for the development of lung cancer. Importantly, these approaches have also uncovered the widespread expression of "noncoding RNAs" including long noncoding RNAs (LncRNAs), which impact biologic responses through the regulation of mRNA transcription or translation. To date, most studies of the role of noncoding RNAs have focused on LncRNAs, which regulate mRNA translation via the RNA interference pathway. Although many of their attributes, such as patterns of expression, remain largely unknown, LncRNAs have key functions in transcriptional, post-transcriptional, and epigenetic gene regulation. Recent research showed that LncRNAs regulate flowering time in the lung cancer. In this review, we discuss these investigations into long noncoding RNAs were performed almost exclusively in lung cancer. Future work will need to extend these into lung cancer and to analyze how LncRNAs interact to regulate mRNA expression. From a clinical perspective, the targeting of LncRNAs as a novel therapeutic approach will require a deeper understanding of their function and mechanism of action.
Collapse
Affiliation(s)
- Hui Tao
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China
| | - Jing-Jing Yang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei 230601, China
| | - Xiao Zhou
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China.
| | - Zi-Yu Deng
- Department of Scientific and Educational, The Second Hospital of Anhui Medical University, China
| | - Kai-Hu Shi
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China.
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| |
Collapse
|
32
|
Postnikova OA, Nemchinov LG. Natural Antisense Transcripts Associated with Salinity Response in Alfalfa. THE PLANT GENOME 2015; 8:eplantgenome2014.09.0057. [PMID: 33228296 DOI: 10.3835/plantgenome2014.09.0057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/09/2015] [Indexed: 06/11/2023]
Abstract
Natural antisense transcripts (NATs) are long noncoding RNAs (lncRNAs) complementary to the messenger (sense) RNA (Wang et al., 2014). Many of them are involved in regulation of their own sense transcripts thus playing pivotal biological roles in all processes of organismal development and responses to the environment. In our previous study, we have identified a number of differentially expressed genes (DEGs) in alfalfa plants (Medicago sativa L.) subjected to salinity stress (Postnikova et al., 2013). In this work, we selected several experimentally validated DEGs identified in response to salt and analyzed them for the presence of NAT pairs. The majority of the examined DEGs encoded NATs. Expression of some NAT pairs changed in response to salinity, suggesting their involvement in regulating the responses of alfalfa to salt.
Collapse
Affiliation(s)
- O A Postnikova
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Lab., 10300 Baltimore Ave., Beltsville, MD, 20705
| | - L G Nemchinov
- USDA-ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Lab., 10300 Baltimore Ave., Beltsville, MD, 20705
| |
Collapse
|
33
|
Aghcheh RK, Kubicek CP. Epigenetics as an emerging tool for improvement of fungal strains used in biotechnology. Appl Microbiol Biotechnol 2015; 99:6167-81. [PMID: 26115753 DOI: 10.1007/s00253-015-6763-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/07/2015] [Accepted: 06/10/2015] [Indexed: 10/23/2022]
Abstract
Filamentous fungi are today a major source of industrial biotechnology for the production of primary and secondary metabolites, as well as enzymes and recombinant proteins. All of them have undergone extensive improvement strain programs, initially by classical mutagenesis and later on by genetic manipulation. Thereby, strategies to overcome rate-limiting or yield-reducing reactions included manipulating the expression of individual genes, their regulatory genes, and also their function. Yet, research of the last decade clearly showed that cells can also undergo heritable changes in gene expression that do not involve changes in the underlying DNA sequences (=epigenetics). This involves three levels of regulation: (i) DNA methylation, (ii) chromatin remodeling by histone modification, and (iii) RNA interference. The demonstration of the occurrence of these processes in fungal model organisms such as Aspergillus nidulans and Neurospora crassa has stimulated its recent investigation as a tool for strain improvement in industrially used fungi. This review describes the progress that has thereby been obtained.
Collapse
Affiliation(s)
- Razieh Karimi Aghcheh
- Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9/166-5, 1060, Vienna, Austria,
| | | |
Collapse
|
34
|
The frequency natural antisense transcript first promotes, then represses, frequency gene expression via facultative heterochromatin. Proc Natl Acad Sci U S A 2015; 112:4357-62. [PMID: 25831497 DOI: 10.1073/pnas.1406130112] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The circadian clock is controlled by a network of interconnected feedback loops that require histone modifications and chromatin remodeling. Long noncoding natural antisense transcripts (NATs) originate from Period in mammals and frequency (frq) in Neurospora. To understand the role of NATs in the clock, we put the frq antisense transcript qrf (frq spelled backwards) under the control of an inducible promoter. Replacing the endogenous qrf promoter altered heterochromatin formation and DNA methylation at frq. In addition, constitutive, low-level induction of qrf caused a dramatic effect on the endogenous rhythm and elevated circadian output. Surprisingly, even though qrf is needed for heterochromatic silencing, induction of qrf initially promoted frq gene expression by creating a more permissible local chromatin environment. The observation that antisense expression can initially promote sense gene expression before silencing via heterochromatin formation at convergent loci is also found when a NAT to hygromycin resistance gene is driven off the endogenous vivid (vvd) promoter in the Δvvd strain. Facultative heterochromatin silencing at frq functions in a parallel pathway to previously characterized VVD-dependent silencing and is needed to establish the appropriate circadian phase. Thus, repression via dicer-independent siRNA-mediated facultative heterochromatin is largely independent of, and occurs alongside, other feedback processes.
Collapse
|
35
|
Meijueiro ML, Santoyo F, Ramirez L, Pisabarro AG. Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies. Brief Funct Genomics 2014; 13:440-50. [DOI: 10.1093/bfgp/elu033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
|