Non-coding RNA in Plants

Modulation and Stress Responses

1st Edition - November 29, 2024
Imprint: Academic Press
Editors: Rahul Datta, Chintan Kapadia, Subhan Danish, Sachidanand Singh
Language: English
Paperback ISBN:
9 7 8 - 0 - 4 4 3 - 2 1 7 8 4 - 5
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 2 1 7 8 5 - 2

Non-coding RNA in Plants: Modulation and Stress Responses  is the first book to present the basics of the importance of long non-coding RNA and its potential in addressin… Read more

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Non-coding RNA in Plants: Modulation and Stress Responses  is the first book to present the basics of the importance of long non-coding RNA and its potential in addressing abiotic and biotic stresses. Describing the MiRNA and small RNA and their role in plant development, this book explains the importance of long non-coding RNA in plants, including its significance in virus resistance, its transposable elements, effector trigger immunity, and fungal and bacterial resistance in plants. Non-coding RNA for Modulation and Stress Response in Plants presents the state-of-the-science from its historical foundation through application throughout the lifecycle and production of agricultural and non-agricultural plants. 

While various coding has been explored within animal science, plant exposition has been minimal.  This book is designed to inspire additional research and developments toward improved plant resiliency and production.

Title of Book
Cover image
Title page
Table of Contents
Copyright
Contributors
Chapter 1. Introduction to long noncoding RNA
Introduction
Epigenetic regulation in long noncoding RNAs and their structure and function
Transposable element derived small noncoding RNA in plants
Database of plant lncRNA
Exploring the future: A glance into ongoing advances
Chapter 2. Regulatory mechanisms and mode of action of non-coding RNA
Introduction
Non-coding RNA
Distinguished between non-coding and coding RNAs
Classification of noncoding RNA
Significance of non-coding RNAs (ncRNAs) in cellular regulation of a plant cell
Role of regulatory ncRNAs in plant stress responses
Role of regulatory ncRNAs in plant growth and development
Emerging significance of non-coding RNAs (ncRNAs) in plant development
miRNAs: Masters of gene regulation
siRNAs: Orchestrators of developmental harmony
LncRNAs: Bridging the regulatory abyss
CircRNAs: Novel players in the developmental symphony
Uncharted territories: Exploring novel ncRNA frontiers
Harnessing the regulatory ncRNAs for crop improvement
Non-coding RNA
MicroRNA (miRNA)
Discovery
Discovery of plant microRNAs (miRNAs)
MicroRNAs (miRNAs) in plant life: Orchestrating growth and responses
Organ-specific regulation
Environmental adaptation
Roles of miRNAs in plant life
Biogenesis regulation
Types of miRNA biogenesis in plant cell
RNA polymerase II (Pol II) recruitment and transcription
Primo miRNAs, or primary miRNA transcripts, and the dicer-like (DCL) family
HEN1-mediated methylation and export to the cytoplasm
RNA-induced silencing complex (RISC)
RISC-mediated regulation of genes
Other methods of processing and noncanonical routes
MicroRNA biogenesis: Insights and distinctions
MicroRNA transcription
Intriguing examples of splicing and miRNA biogenesis
Implications of splicing on miRNA biogenesis
Plant pri-miRNA processing: Orchestrating accuracy and efficiency
Pri-miRNA structural diversity
Determinants of Pri-miRNA processing
Influential proteins in pri-miRNA processing
Modes of pri-miRNA processing
Co-transcriptional processing dynamics
Pri-miRNA degradation: Efficient clearance mechanisms
Regarding the regulation of microRNA 3′-end modification
The NEXT complex contributes to the degradation of miRNA precursors
Both degradation pathways compete with the microprocessor for pri-miRNAs
Degradation of pri-miRNA byproducts
miRNA stability
RISC formation
RISC complex formation
AGO1 protein in plants
AGO protein's structure
Involvement of AGO1 in transcriptional suppression
Regulation of miRNA biogenesis
Molecular chaperone Hsp90
Involvement of SQN in miRNA silencing
Importin-β proteins EMA1 and TRN1
miRNA export in plants: insights and mechanisms
Historical perspective
Export mechanisms
Regulatory proteins
Long-distance regulation
Interactions with other organisms
Evolutionary conservation
Small interfering RNA (siRNA)
Overview of siRNA
Similarities and differences between miRNA and siRNA
Role in gene silencing and RNA interference
Long non-coding RNA (lncRNA)
Characteristics of lncRNA
Functions and mechanisms of action
Examples of lncRNA involvement in cellular processes
Small nuclear RNA (snRNA) in plant cells
Role in RNA splicing
Other types of non-coding RNA (ncRNA) in plant cells
Piwi-interacting RNA (piRNA)
Small nucleolar RNA (snoRNA)
Other types of ncRNA
Regulatory mechanisms
Post-transcriptional regulation by ncRNA in plant cells
Interactions of ncRNA with proteins in plant cells
Functional significance of ncRNA in plant cells
Disease implications of ncRNA dysregulation in plant cells
Techniques for studying ncRNA in plant cells
Challenges and advancements
Future directions in ncRNA research
Chapter 3. Bioinformatic database, artificial intelligence and machine learning-based tools for non-coding RNA study
Introduction
Database for RNA study
RNAcentral: The Universal Compendium (Sweeney et al., 2019)
NONCODEv5: The LncRNA mastermind (Fang et al., 2018)
miRBase: The microRNA maestro (Kozomara et al., 2019)
lncRNAdb: The disease decoder (Quek et al., 2015)
starBase: The network weaver (Li et al., 2014)
LINCipedia: LncRNA masterclass (Volders et al., 2013)
cisTarget: Unveiling cis-regulatory landscapes (Stein Aerts lab, 2022)
NONCODE2016: A historical compass (Zhao et al., 2016)
FANTOM: Granular expression atlas (Abugessaisa et al., 2021)
evofold: Decoding the structural code (Pedersen et al., 2006)
CRIPSRlnc: Precise LncRNA manipulation (Cheng and Qiu, 2018)
RAID: Charting the RNA-RNA interactome (Lin et al., 2020)
NONCODE v6.0 (beta): A glimpse of the future (Zhao et al., 2021)
Web tool for RNA structure prediction and study: Unveiling the hidden language of RNA
Algorithms for RNA folding
Webtools: Democratizing access to computational power
RNAfold
Integration of AI in RNA structure prediction
Role of AI, ML and deep learning with RNA research
Flow art for RNA-based computational study with AI
From prediction to creation: Engineering ncRNAs with AI precision
Unveiling hidden networks: Demystifying ncRNA interactions with AI
Bridging the gap: From bench to bedside with AI-driven ncRNA therapeutics and diagnostics
Future of RNA-based computational biology with artificial intelligence
Design with precision: Engineering ncRNAs for tailored functionality
Unveiling hidden networks: Demystifying ncRNA interactions with AI
From petri dish to patient: Charting the AI-driven ncRNA therapeutics and diagnostics
Unlocking the secrets of disease: Precision diagnostics with ncRNA fingerprints
Tailoring treatment: Targeting diseases with AI-designed ncRNA therapeutics
Navigating the labyrinth: AI as a map to ncRNA function
Optimizing safety: Overcoming hurdles with AI-powered design
Exploring the future: A glimpse into ongoing advances
Chapter 4. Fertilizer-responsive non-coding RNA and their significance
Introduction to fertilizer-responsive non-coding RNA
Importance of fertilizer responsiveness
Role of non-coding RNA in fertilizer response
Mechanisms of non-coding RNA action
Types of fertilizer-responsive non-coding RNA
MicroRNAs (miRNAs)
Long non-coding RNAs (lncRNAs)
Circular RNAs (circRNAs)
Other emerging classes
Integration and interplay among ncRNA classes
Regulatory networks and signaling pathways
Fertilizer-induced regulatory networks
Non-coding RNA as molecular signals
Impact on agricultural practices
Precision nutrient management
Crop improvement and genetic engineering
Sustainable agriculture and environmental conservation
Innovative biotechnological applications
Shaping future agricultural paradigms
Enhancing crop yield and quality
Sustainable agriculture through RNA applications
Biotechnological applications and innovations
Non-coding RNA in biotechnology
Engineering fertilizer-responsive RNA constructs
Challenges and limitations
Unexplored frontiers in RNA-mediated responses
Addressing technological and practical constraints
Future directions in research
Conclusion
Chapter 5. Role of non-coding RNA in plant architecture
Introduction
Types and classification of non-coding RNAs
microRNAs (miRNAs)
Role in regulating plant architecture
Small interfering RNAs (siRNAs)
Mechanisms of action
Influence on plant morphology and development
Long non-coding RNAs (lncRNAs)
Characteristics and diversity
Implications for plant architecture
Regulatory mechanisms of ncRNA in plant architecture
Regulation of gene expression using ncRNA-mediated mechanisms
Interactions between ncRNAs and target genes
Signaling networks and pathways involving ncRNAs in shaping plant structure
Functional roles of ncRNA in plant growth and development
Influence of ncRNAs on shoot and root development
Modulation of branching patterns and leaf morphology
Impact of ncRNAs on flower and fruit development
Experimental techniques and tools for studying ncRNA in plant architecture
Transcriptomic and bioinformatic approaches
CRISPR/Cas9-based methods for ncRNA functional analysis
Imaging and visualization techniques for ncRNA localization
Emerging trends and future directions
Potential applications in crop improvement and breeding
Unexplored areas and research gaps in understanding ncRNA-mediated plant architecture
Technological advancements and their impact on studying ncRNA functions
Conclusion
Chapter 6. Non-coding RNA and its significance to virus resistance in plants
Introduction
Plant-virus interactions
Plant defense system against viral pathogen
Non-coding RNAs (ncRNAs)
Identification of ncRNAs
Long non-coding RNAs (lncRNAs): Masters of cellular regulation
Deciphering mode of action and genetic regulation for immunity by lncRNAs
Role of non-coding RNA to virus resistance in plants
siRNAs
miRNAs
LncRNAs
Challenges
Future thrust
Conclusion
Chapter 7. Unveiling the role of non-coding RNAs in abiotic stress adaptation
Introduction
Classification and biosynthesis of non-coding RNA
Role of non-coding RNA in gene regulation
Role of non-coding RNA in abiotic stress responses
Cereals
Pulses
Oil seeds
Millets
Online database for exploring ncRNAs
Bioinformatic tools for exploring ncRNAs
Conclusion and future perspectives
Chapter 8. Transposable element derived non-coding RNA and its significance
Introduction
Biogenesis
Transposable element derived small noncoding RNA in plants
Transposable element derived long noncoding RNA in plants
Classification of transposable element-derived small noncoding RNAs
Heterochromatic siRNA generated from transposable elements that act in trans
Epigenetically active siRNA generated from transposable elements that act in trans
Classification of transposable element-derived long noncoding RNAs
LncRNAs from TEs as sources of RNA and regulators of protein
LncRNAs from TEs as possible controllers of chromatin conformation
Significance of transposable element-derived non-coding RNA
In-plant gene regulation
In plants reproduction and hybridization
In the modulation and stress response management in plants
Future prospects
Conclusion
Chapter 9. Role of non coding RNA in effector trigger immunity
Introduction
Types of ncRNA involved in ETI
microRNAs (miRNAs)
Role in modulating ETI signaling pathways
Examples of miRNAs involved in ETI
Long non-coding RNAs (lncRNAs)
Role in regulating ETI-associated gene expression
Examples of lncRNAs implicated in ETI
Small interfering RNAs (siRNAs)
Participation in antiviral defense mechanisms
Impact on ETI regulation
Mechanisms of ncRNA-mediated regulation in ETI
Targeting of mRNAs encoding immune regulators
Epigenetic modulation of gene expression
Crosstalk with other immune signaling pathways
Experimental evidence supporting the involvement of ncRNAs in ETI
Transcriptomic analysis of ncRNA expression during ETI
Functional studies using ncRNA mutants or knockdowns
Cross-species comparisons revealing conservation of ncRNA-mediated ETI mechanisms
Future perspectives and challenges
Potential therapeutic applications targeting ncRNA in ETI modulation
Technological advancements needed for elucidating ncRNA functions in ETI
Limitations and gaps in current understanding
Conclusion
Chapter 10. Noncoding RNAs properties and biological functions in plant development and abiotic stress response
Introduction
Classification of ncRNAs and their properties
Circular ncRNAs (circRNAs)
Linear ncRNAs
Housekeeping ncRNAs
Regulatory ncRNAs
Interactions and networks of non-coding RNAs in plants
Functional roles of ncRNAs in plant abiotic stress
Extreme temperatures
Salinity
Metal toxicity
Water scarcity
Functional role of ncRNAs in plant development
Vernalization
Photomorphogenesis
Anther, pollen and seed development
Root organogenesis, node formation and fiber development
Phosphate homeostasis, plant regeneration and immunity
Applications of non-coding RNAs
Chapter 11. Noncoding RNA and its significance in fungal and bacterial resistance
Introduction
Significant roles of ncRNAs in different biotic stress reactions
Significance of non-coding RNAs as a defense against fungal infection
Significance of non-coding RNAs as a defense against bacterial infection
Conclusion
Chapter 12. Non-coding RNA and hormonal regulation in plants
Introduction
Non-coding RNAs
Long non-coding RNAs
Biogenesis of lncRNAs
Types of lncRNAs
lncRNAs regulate plant physiological processes by mediating phytohormone signaling
Auxin
Cytokinin
Gibberellin
Ethylene
Abscisic acid
Jasmonic acid
Salicylic acid
Brassinosteroids
Conclusion
Future perspectives
Chapter 13. Fruits ripening and maturity: Role of non-coding RNA
Introduction
Climate-related and non-climatic ripening
Common genetic regulatory processes control the ripening of fruits
Fruit ripening controlled by molecular/hormonal signals
Non-coding RNAs that regulate fruit ripening
The physiological as well as biochemical factors that influence fruit ripening: Controlled genes
Non coding RNA in fruit ripening
Noncoding RNAs regulatory networks
Non coding RNA: Ethylene regulatory activity
Non coding RNA: Fruit coloring
Non coding RNA: Fruit flavor
Non coding RNA: Fruit texture
Conclusion and future perspectives
Chapter 14. Non-coding RNA as a regulator for developmental processes in plants
Introduction
The integral role of miRNAs in plant development
siRNA in plant development
lncRNAs are involved in vegetative growth
Root growth and development
Leaf development
Photomorphogenesis
Phytohormone regulation
Concluding remarks
Chapter 15. Modulation of non-coding RNA at the reproductive stage of plants
Introduction
Non-coding RNA modulation and regulatory roles across plant reproductive stages
Gamete formation
Pollination
Fertilization and seed germination
Floral development
Conclusion and future prospect
Chapter 16. Cross kingdom application of noncoding RNA
Introduction
Natural cross kingdom RNA transfer
Extracellular vesicles and small RNA transport
Spray induced gene silencing or exogenous RNA application
Host induced gene silencing as a proof of concepts
Conclusion
Chapter 17. Advantages and limitations of exogenously supplied non-coding RNA in plants
Introduction
MicroRNAs (miRNAs)
Small interfering RNAs (siRNAs)
Long non-coding RNAs (lncRNAs)
Concept of environmental RNAi
Evidences of natural exogenous non coding RNA uptake in plants
Inducing PTGS using exogenously supplied non coding RNAs
Impact of exogenously supplied ncRNAs in abiotic stress
Impact of exogenously supplied ncRNAs in biotic stress
Crop improvement strategies using exogenously supplied small RNAs
Conclusion
Chapter 18. Epigenetic modulation of plant developmental pathways by non-coding RNA
Introduction
Mechanisms of plant epigenetic regulation
DNA methylation (DM)
Histone methylation (HiM)
RNA-mediated silencing of genes (RMSG)
Chromatin remodeling complexes (CRCs)
Housekeeping ncRNAs
Regulatory ncRNAs
Applications of non coding RNA in plants
Photosensitive male sterility (PSMS)
Vernalization
Photomorphogenesis
Formation of nodules
Phosphate absorption
Biosynthesis of secondary plant products
Biotic and abiotic stresses
Processed fruit ripening
Databases for identifying plants non coding RNA
lncRNA INVESTMENT
Investigation of miRNAs
Investigation of circRNA
Challenges and conclusion
Index

Rahul Datta

Dr Rahul Datta is Asst. Professor in the field of Soil Science currently is working at Mendel University in Brno, Czech Republic. His research has focused largely on increasing crop productivity using “green” and sustainable methods. Some of the most notable problems he has addressed through his research are drought stress, heavy metal toxicity in soil, and climate change greenhouse gas. His research has helped in increasing the quality and productivity of staple crops like wheat maize, barley, rice, and other crops like mangoes, spinach, and cotton. His work has been cited in excess of 2200 times. He has published extensively and is an editorial board member of the journals PlosOne, Sustainability (MDPI), BMC Plant Biology and Open Agriculture, in which he is overseeing a special issue on current trends in agriculture (MDPI). At present, He is also a member of the Soil Science Society of America.

Affiliations and expertise

Department of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Czech Republic

Chintan Kapadia

Dr. Chintan Kapadia is an Assistant Professor in the Department of Plant Molecular Biology and Biotechnology, Aspee College of Horticulture and Forestry, Navsari Agricultural University, Navsari, Gujarat India. He obtained his Ph.D. degree from Navsari Agricultural University in the discipline of Plant Biotechnology. He has been working in the field of Plant biotechnology for 11 years and he has worked on the Micro RNA involved in the resistance of eggplant towards Ralstonia solanacerum infection. His main research area includes metagenomics, microbial biodiversity analysis, Sequencing, Restoration Ecology, Genomics, Bioinformatics, Plant Stress Biology, Molecular Mechanisms for Plant-Insect interaction, MicroRNA and plant Microbes Interaction, Plant Growth Promoting Molecules such as Siderophore and organic acids, Relationship between nutrient-limiting environment and phage lysogeny, carbon assimilation pathways in microbes and Microalgal-based biofuel..

Affiliations and expertise

Department of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture and Forestry, Navsari Agricultural University, Navsari, Gujarat, India

Subhan Danish

Dr Subhan Danish has a bachelor’s degree in Agriculture, and master’s and doctorate degrees in Agriculture (Soil Science). He is currently teaching at Bahauddin Zakariya University and Mendel University in Brno as a guest lecturer. He teaches at the undergraduate and graduate levels, focusing on soil science and plant nutrition. His current research interests include soil science and plant nutrition, abiotic stress alleviation, nanoparticles in agriculture and climate-smart agriculture with artificial intelligence. His papers were published in a variety of peer-reviewed journals (e.g., Scientific Report, Journal of Environmental Management, Science of the Total Environment, Cleaner Production, Chemosphere etc).

Affiliations and expertise

Pesticide Quality Control Laboratory, Agriculture Complex, Old Shujabad Road, Multan, Punjab, Pakistan

Sachidanand Singh

Dr. Sachidanand Singh, B.Tech Biotechnology, M.Tech Bioinformatics and PhD in Bioinformatics. He has a postdoctoral research experience from college of Pharmacy, Ohio State University, USA. His specialization area includes Plant Biotechnology, Systems Biology and Drug design. He has more than 12 years of research and academic experience. He has published extensively, including on plant-based studies in association to Soil microbiome, herbal drug formulation, drug design and microbe-microbe interactions and their expression-based studies. He has served for a decade in School of Biotechnology and Health Sciences, Karunya University, Coimbatore, Tamil Nadu, India. He also worked as consultant for college of pharmacy, Ohio State University as a Statistical Genetics during the year 2018. He has published in peer reviewed journals.

Affiliations and expertise

Associate Professor, Department of Biotechnology, School of Energy and Technology, Pandit Deendayal Energy University, Gujarat, India.

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Non-coding RNA in Plants

Modulation and Stress Responses

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Rahul Datta

Chintan Kapadia

Subhan Danish

Sachidanand Singh

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