Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

Abstract Background Long non-coding RNAs (lncRNAs) are regulatory transcripts of length > 200 nt. Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal defense networks. Therefore, we investigated their role in Vitis vinifera (grapevine) in response to obligate biotrophic fungal phytopathogens, Erysiphe necator (powdery mildew, PM) and Plasmopara viticola (downy mildew, DM), which impose huge agro-economic burden on grape-growers worldwide. Results Using computational approach based on RNA-seq data, 71 PM- and 83 DM-responsive V. vinifera lncRNAs were identified and comprehensively examined for their putative functional roles in plant defense response. V. vinifera protein coding sequences (CDS) were also profiled based on expression levels, and 1037 PM-responsive and 670 DM-responsive CDS were identified. Next, co-expression analysis-based functional annotation revealed their association with gene ontology (GO) terms for ‘response to stress’, ‘response to biotic stimulus’, ‘immune system process’, etc. Further investigation based on analysis of domains, enzyme classification, pathways enrichment, transcription factors (TFs), interactions with microRNAs (miRNAs), and real-time quantitative PCR of lncRNAs and co-expressing CDS pairs suggested their involvement in modulation of basal and specific defense responses such as: Ca2+-dependent signaling, cell wall reinforcement, reactive oxygen species metabolism, pathogenesis related proteins accumulation, phytohormonal signal transduction, and secondary metabolism. Conclusions Overall, the identified lncRNAs provide insights into the underlying intricacy of grapevine transcriptional reprogramming/post-transcriptional regulation to delay or seize the living cell-dependent pathogen growth. Therefore, in addition to defense-responsive genes such as TFs, the identified lncRNAs can be further examined and leveraged to candidates for biotechnological improvement/breeding to enhance fungal stress resistance in this susceptible fruit crop of economic and nutritional importance.

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393 DECONVOLUTING THE COMPLEXITY OF LONG NON-CODING RNAS AND ESOPHAGEAL CARCINOMA FOR POTENTIAL CLINICAL IMPLICATIONS

Diseases of the Esophagus ◽

10.1093/dote/doab052.393 ◽

2021 ◽

Vol 34 (Supplement_1) ◽

Author(s):

Siyuan Luan ◽

Yushang Yang ◽

Shouyue Zhang ◽

Xiaoxi Zeng ◽

Xin Xiao ◽

...

Keyword(s):

Esophageal Carcinoma ◽

Rapid Development ◽

Direct Interaction ◽

Clinical Applications ◽

Regulatory Mechanisms ◽

Protein Coding ◽

Functional Roles ◽

Cancer Hallmarks ◽

Clinical Scenarios ◽

Non Coding Rnas

Abstract Long non-coding RNAs (lncRNAs), a type of transcriptional products with more than 200 nucleotides in length, have been less characterized compared to protein-coding RNAs so far. However, it is increasingly evident that lncRNAs are key players involved in multiple genetic and epigenetic activities during the carcinogenesis of neoplastic diseases. Currently, accumulating data have pointed out the close connection between lncRNAs and esophageal carcinoma (EC), shedding light on further unravelling the complexity of lncRNAs and EC. Methods In this review, we thoroughly collect the evidence regarding original studies on EC-related lncRNAs by searching in MEDLINE/PubMed, Embase and WOS/SCI. We especially focus on summarizing EC-related lncRNAs based upon more updated evidence, and further discuss their different features from various perspectives, including regulatory mechanisms, functional roles in cancer hallmarks, as well as potential diagnostic and therapeutic applications, which would together reveal the complexity of lncRNAs and EC for potential clinical applications. Results We discuss over thirty EC-related lncRNAs in total, most of which function as oncogenes that promote cancer development, while the others function as tumor suppressors. Regulatory mechanisms included sponging miRNAs, direct interaction with proteins, and exosome visicle-based intercellular communication. Based upon these modes of actions, lncRNAs play multiple roles in cancer hallmarks such as uncontrolled cell growth, evasion of programmed cell death, invasion and metastasis. Moreover, lncRNAs packaged in exosomes have unique potency to serve as diagnostic biomarkers; some lncRNAs show great potential to predict patients' chemical resistance and may be crucial targets to improve chemoradiotherapy and targeted therapy. Conclusion Over the past few years, the research of EC-related lncRNAs maintain obviously rapid development, yet further exploration of exact mechanisms and clinical applications that lncRNAs can offer need to be done. Indeed, LncRNAs hold the promise of being applied in multiple clinical scenarios, especially early diagnosis of EC, improvement of sensitivity to chemotherapy/radiotherapy, and development of small-molecule targeted drugs.

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Long Non-Coding RNAs and Related Molecular Pathways in the Pathogenesis of Epilepsy

International Journal of Molecular Sciences ◽

10.3390/ijms20194898 ◽

2019 ◽

Vol 20 (19) ◽

pp. 4898 ◽

Cited By ~ 5

Author(s):

Villa ◽

Lavitrano ◽

Combi

Keyword(s):

Biological Processes ◽

Complete Understanding ◽

Aberrant Expression ◽

Protein Coding ◽

Diagnostic Biomarkers ◽

Functional Roles ◽

The Central Nervous System ◽

Non Coding Rnas ◽

Underlying Mechanisms ◽

Coding Capacity

Epilepsy represents one of the most common neurological disorders characterized by abnormal electrical activity in the central nervous system (CNS). Recurrent seizures are the cardinal clinical manifestation. Although it has been reported that the underlying pathological processes include inflammation, changes in synaptic strength, apoptosis, and ion channels dysfunction, currently the pathogenesis of epilepsy is not yet completely understood. Long non-coding RNAs (lncRNAs), a class of long transcripts without protein-coding capacity, have emerged as regulatory molecules that are involved in a wide variety of biological processes. A growing number of studies reported that lncRNAs participate in the regulation of pathological processes of epilepsy and they are dysregulated during epileptogenesis. Moreover, an aberrant expression of lncRNAs linked to epilepsy has been observed both in patients and in animal models. In this review, we summarize latest advances concerning the mechanisms of action and the involvement of the most dysregulated lncRNAs in epilepsy. However, the functional roles of lncRNAs in the disease pathogenesis are still to be explored and we are only at the beginning. Additional studies are needed for the complete understanding of the underlying mechanisms and they would result in the use of lncRNAs as diagnostic biomarkers and novel therapeutic targets.

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Characterization and Analysis of Whole Transcriptome of Giant Panda Spleens: Implying Critical Roles of Long Non-Coding RNAs in Immunity

Cellular Physiology and Biochemistry ◽

10.1159/000488837 ◽

2018 ◽

Vol 46 (3) ◽

pp. 1065-1077 ◽

Cited By ~ 6

Author(s):

Rui Peng ◽

Yuliang Liu ◽

Zhigang Cai ◽

Fujun Shen ◽

Jiasong Chen ◽

...

Keyword(s):

Giant Panda ◽

Pathological Condition ◽

Species Conservation ◽

Large Set ◽

Illumina Hiseq ◽

Protein Coding ◽

Giant Pandas ◽

Functional Roles ◽

Non Coding Rnas ◽

Mirna Sponges

Background/Aims: Giant pandas, an endangered species, are a powerful symbol of species conservation. Giant pandas may suffer from a variety of diseases. Owing to their highly specialized diet of bamboo, giant pandas are thought to have a relatively weak ability to resist diseases. The spleen is the largest organ in the lymphatic system. However, there is little known about giant panda spleen at a molecular level. Thus, clarifying the regulatory mechanisms of spleen could help us further understand the immune system of the giant panda as well as its conservation. Methods: The two giant panda spleens were from two male individuals, one newborn and one an adult, in a non-pathological condition. The whole transcriptomes of mRNA, lncRNA, miRNA, and circRNA in the two spleens were sequenced using the Illumina HiSeq platform. EBseq and IDEG6 were used to observe the differentially expressed genes (DEGs) between these two spleens. Gene Ontology and KEGG analyses were used to annotate the function of DEGs. Furthermore, networks between non-coding RNAs and protein-coding genes were constructed to investigate the relationship between non-coding RNAs and immune-associated genes. Results: By comparative analysis of the whole transcriptomes of these two spleens, we found that one of the major roles of lncRNAs could be involved in the regulation of immune responses of giant panda spleens. In addition, our results also revealed that microRNAs and circRNAs may have evolved to regulate a large set of biological processes of giant panda spleens, and circRNAs may function as miRNA sponges. Conclusion: To our knowledge, this is the first report of lncRNAs and circRNAs in giant panda, which could be a useful resource for further giant panda research. Our study reveals the potential functional roles of miRNAs, lncRNAs, and circRNAs in giant panda spleen.

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Characterisation and functional predictions of canine long non-coding RNAs

10.1101/303966 ◽

2018 ◽

Author(s):

Céline Le Béguec ◽

Valentin Wucher ◽

Lætitia Lagoutte ◽

Edouard Cadieu ◽

Nadine Botherel ◽

...

Keyword(s):

Expression Profiles ◽

Expression Patterns ◽

Regulatory Elements ◽

Domestic Dog ◽

Tissue Type ◽

Protein Coding ◽

Functional Roles ◽

Integrative Study ◽

Non Coding Rnas ◽

Biological Functionality

AbstractLong non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and humans through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.

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SALTS – SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite

10.1101/2021.02.08.430280 ◽

2021 ◽

Author(s):

Mohan V Kasukurthi ◽

Dominika Houserova ◽

Yulong Huang ◽

Addison A. Barchie ◽

Justin T. Roberts ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Protein Coding ◽

Web Based ◽

Functional Roles ◽

Sequencing Technologies ◽

Active Research ◽

The Cost ◽

Analysis Platform ◽

Transcriptional Output

ABSTRACTThe widespread utilization of high-throughput sequencing technologies has unequivocally demonstrated that eukaryotic transcriptomes consist primarily (>98%) of non-coding RNA (ncRNA) transcripts significantly more diverse than their protein-coding counterparts.ncRNAs are typically divided into two categories based on their length. (1) ncRNAs less than 200 nucleotides (nt) long are referred as small non-coding RNAs (sncRNAs) and include microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), transfer ribonucleic RNAs (tRNAs), etc., and the majority of these are thought to function primarily in controlling gene expression. That said, the full repertoire of sncRNAs remains fairly poorly defined as evidenced by two entirely new classes of sncRNAs only recently being reported, i.e., snoRNA-derived RNAs (sdRNAs) and tRNA-derived fragments (tRFs). (2) ncRNAs longer than 200 nt long are known as long ncRNAs (lncRNAs). lncRNAs represent the 2nd largest transcriptional output of the cell (behind only ribosomal RNAs), and although functional roles for several lncRNAs have been reported, most lncRNAs remain largely uncharacterized due to a lack of predictive tools aimed at guiding functional characterizations.Importantly, whereas the cost of high-throughput transcriptome sequencing is now feasible for most active research programs, tools necessary for the interpretation of these sequencings typically require significant computational expertise and resources markedly hindering widespread utilization of these datasets. In light of this, we have developed a powerful new ncRNA transcriptomics suite, SALTS, which is highly accurate, markedly efficient, and extremely user-friendly. SALTS stands for SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite and offers platforms for comprehensive sncRNA and lncRNA profiling and discovery, ncRNA functional prediction, and the identification of significant differential expressions among datasets. Notably, SALTS is accessed through an intuitive Web-based interface, can be used to analyze either user-generated, standard next-generation sequencing (NGS) output file uploads (e.g., FASTQ) or existing NCBI Sequence Read Archive (SRA) data, and requires absolutely no dataset pre-processing or knowledge of library adapters/oligonucleotides.SALTS constitutes the first publically available, Web-based, comprehensive ncRNA transcriptomic NGS analysis platform designed specifically for users with no computational background, providing a much needed, powerful new resource capable of enabling more widespread ncRNA transcriptomic analyses. The SALTS WebServer is freely available online at http://salts.soc.southalabama.edu.

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Rpv Mediated Defense Responses in Grapevine Offspring Resistant to Plasmopara viticola

Plants ◽

10.3390/plants9060781 ◽

2020 ◽

Vol 9 (6) ◽

pp. 781

Author(s):

Tyrone Possamai ◽

Daniele Migliaro ◽

Massimo Gardiman ◽

Riccardo Velasco ◽

Barbara De Nardi

Keyword(s):

Downy Mildew ◽

Cost Effective ◽

Plasmopara Viticola ◽

Defense Responses ◽

Resistance Level ◽

Resistance Response ◽

Host Pathogen Interaction ◽

Resistant Varieties ◽

New Varieties ◽

Independent Features

Downy mildew, caused by the biotrophic oomycete Plasmopara viticola, is one of the most serious grapevine diseases. The development of new varieties, showing partial resistance to downy mildew, through traditional breeding provides a sustainable and effective solution for disease management. Marker-assisted-selection (MAS) provide fast and cost-effective genotyping methods, but phenotyping remains necessary to characterize the host–pathogen interaction and assess the effective resistance level of new varieties as well as to validate MAS selection. In this study, the Rpv mediated defense responses were investigated in 31 genotypes, encompassing susceptible and resistant varieties and 26 seedlings, following inoculation of leaf discs with P. viticola. The offspring differed in Rpv loci inherited (none, one or two): Rpv3-3 and Rpv10 from Solaris and Rpv3-1 and Rpv12 from Kozma 20-3. To improve the assessment of different resistance responses, pathogen reaction (sporulation) and host reaction (necrosis) were scored separately as independent features. They were differently expressed depending on Rpv locus: offspring carrying Rpv3-1 and Rpv12 loci showed the strongest resistance response (scarce sporulation and necrosis), those carrying Rpv3-3 locus showed the highest levels of necrosis while Rpv10 carrying genotypes showed intermediate levels of both sporulation and necrosis.

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Non-Coding RNAs and their Integrated Networks

Journal of Integrative Bioinformatics ◽

10.1515/jib-2019-0027 ◽

2019 ◽

Vol 16 (3) ◽

Cited By ~ 16

Author(s):

Peijing Zhang ◽

Wenyi Wu ◽

Qi Chen ◽

Ming Chen

Keyword(s):

Gene Regulatory Networks ◽

Regulatory Networks ◽

Protein Coding ◽

Integrated Networks ◽

Cellular Processes ◽

Sequencing Technologies ◽

Different Types ◽

Gene Regulatory ◽

Non Coding Rnas ◽

Eukaryotic Genomes

AbstractEukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs’ essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.

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In silico prediction of long intergenic non-coding RNAs in sheep

Genome ◽

10.1139/gen-2015-0141 ◽

2016 ◽

Vol 59 (4) ◽

pp. 263-275 ◽

Cited By ~ 16

Author(s):

Mohammad Reza Bakhtiarizadeh ◽

Batool Hosseinpour ◽

Babak Arefnezhad ◽

Narges Shamabadi ◽

Seyed Alireza Salami

Keyword(s):

Limb Development ◽

Striated Muscle ◽

Gc Content ◽

Ovis Aries ◽

Specific Expression ◽

Protein Coding ◽

Rna Molecules ◽

Sequencing Technologies ◽

Non Coding Rnas ◽

Organismal Development

Long non-coding RNAs (lncRNAs) are transcribed RNA molecules >200 nucleotides in length that do not encode proteins and serve as key regulators of diverse biological processes. Recently, thousands of long intergenic non-coding RNAs (lincRNAs), a type of lncRNAs, have been identified in mammalians using massive parallel large sequencing technologies. The availability of the genome sequence of sheep (Ovis aries) has allowed us genomic prediction of non-coding RNAs. This is the first study to identify lincRNAs using RNA-seq data of eight different tissues of sheep, including brain, heart, kidney, liver, lung, ovary, skin, and white adipose. A computational pipeline was employed to characterize 325 putative lincRNAs with high confidence from eight important tissues of sheep using different criteria such as GC content, exon number, gene length, co-expression analysis, stability, and tissue-specific scores. Sixty-four putative lincRNAs displayed tissues-specific expression. The highest number of tissues-specific lincRNAs was found in skin and brain. All novel lincRNAs that aligned to the human and mouse lincRNAs had conserved synteny. These closest protein-coding genes were enriched in 11 significant GO terms such as limb development, appendage development, striated muscle tissue development, and multicellular organismal development. The findings reported here have important implications for the study of sheep genome.

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Nonhost Versus Host Resistance to the Grapevine Downy Mildew, Plasmopara viticola, Studied at the Tissue Level

Phytopathology ◽

10.1094/phyto-98-7-0776 ◽

2008 ◽

Vol 98 (7) ◽

pp. 776-780 ◽

Cited By ~ 58

Author(s):

A. M. Díez-Navajas ◽

S. Wiedemann-Merdinoglu ◽

C. Greif ◽

D. Merdinoglu

Keyword(s):

Downy Mildew ◽

Host Specificity ◽

Plasmopara Viticola ◽

Defense Responses ◽

Tissue Level ◽

Vitis Riparia ◽

Grapevine Downy Mildew ◽

Resistance Factors ◽

Clear Cut ◽

Muscadinia Rotundifolia

Following inoculation of host and nonhost plants with Plasmopara viticola, the grapevine downy mildew, a histological survey was undertaken to identify the stage where its development is contained in nonhosts and in resistant host plants. Three herbaceous nonhost species, Beta vulgaris, Lactuca sativa, and Capsicum annuum, and three grapevine species displaying different level of resistance (Vitis vinifera [susceptible], Vitis riparia [partially resistant] and Muscadinia rotundifolia [totally resistant]) where inoculated by P. viticola using a controlled leaf disk inoculation bioassay. During the early steps of infection, defined as encystment of zoospores on stomata, penetration of the germ tube, and production of the vesicle with the primary hypha, there was no evidence of a clear-cut preference to grapevine tissues that could attest to host specificity. The main difference between host grapevine species and nonhosts was observed during the haustorium formation stage. In nonhost tissues, the infection was stopped by cell wall-associated defense responses before any mature haustorium could appear. Defense responses in resistant grapevines were triggered when haustoria were fully visible and corresponded to hypersensitive responses. These observations illustrate that, for P. viticola, haustorium formation is not only a key stage for the establishment of biotrophy but also for the host specificity and the recognition by grapevine resistance factors.

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Grapevine Rpv3-, Rpv10- and Rpv12-mediated defense responses against Plasmopara viticola and the impact of their deployment on fungicide use in viticulture

BMC Plant Biology ◽

10.1186/s12870-021-03228-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Chantal Wingerter ◽

Birgit Eisenmann ◽

Patricia Weber ◽

Ian Dry ◽

Jochen Bogs

Keyword(s):

Cell Death ◽

Downy Mildew ◽

Plant Protection ◽

Resistance Mechanism ◽

Plasmopara Viticola ◽

Defense Responses ◽

Natural Resistance ◽

Detailed Knowledge ◽

Infection Pressure ◽

The Impact

Abstract Background The high susceptibility of European grapevine cultivars (Vitis vinifera) to downy mildew (Plasmopara viticola) leads to the intensive use of fungicides in viticulture. To reduce this input, breeding programs have introgressed resistance loci from wild Vitis species into V. vinifera, resulting in new fungus-resistant grapevine cultivars (FRC). However, little is known about how these different resistance loci confer resistance and what the potential reduction in fungicide applications are likely to be if these FRCs are deployed. To ensure a durable and sustainable resistance management and breeding, detailed knowledge about the different defense mechanisms mediated by the respective Rpv (Resistance to P. viticola) resistance loci is essential. Results A comparison of the resistance mechanisms mediated by the Rpv3–1, Rpv10 and/or Rpv12-loci revealed an early onset of programmed cell death (PCD) at 8 hours post infection (hpi) in Rpv12-cultivars and 12 hpi in Rpv10-cultivars, whereas cell death was delayed in Rpv3-cultivars and was not observed until 28 hpi. These temporal differences correlated with an increase in the trans-resveratrol level and the formation of hydrogen peroxide shortly before onset of PCD. The differences in timing of onset of Rpv-loci specific defense reactions following downy mildew infection could be responsible for the observed differences in hyphal growth, sporulation and cultivar-specific susceptibility to this pathogen in the vineyard. Hereby, Rpv3- and Rpv12/Rpv3-cultivars showed a potential for a significant reduction of fungicide applications, depending on the annual P. viticola infection pressure and the Rpv-loci. Furthermore, we report on the discovery of a new P. viticola isolate that is able to overcome both Rpv3- and Rpv12-mediated resistance. Conclusion This study reveals that differences in the timing of the defense reaction mediated by the Rpv3-, Rpv10- and Rpv12-loci, result in different degrees of natural resistance to downy mildew in field. Vineyard trials demonstrate that Rpv12/Rpv3- and Rpv3-cultivars are a powerful tool to reduce the dependence of grape production on fungicide applications. Furthermore, this study indicates the importance of sustainable breeding and plant protection strategies based on resistant grapevine cultivars to reduce the risk of new P. viticola isolates that are able to overcome the respective resistance mechanism.

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