Guleria, P: Plant Small RNA

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Plant
Small RNA:
Biogenesis, Regulation
and Application
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Contributors
Section 1: Basics
1
Introduction to plant small RNAs
	Introduction
	Discovery history of small RNAs
	Diversity of small RNAs
		miRNAs
			Biogenesis of plant miRNAs
			miRNA turnover
			Mode of action of miRNAs
				miRNA-guided transcript cleavage
				miRNA-mediated translation repression
			miRNAs in plant development
				miRNA-mediated regulation of meristem organization and cell polarity
				miRNA-mediated regulation of flower development
				miRNA-mediated regulation of root architecture
				miRNA-mediated regulation of seed development
		siRNAs
			Biogenesis of siRNAs
			Mode of action of siRNAs
			Biological functions of 24-nt transposable element (TE)-derived siRNAs
		phasiRNAs
			Biogenesis of phasiRNAs
			Biological functions of phasiRNAs
	Movement of small RNAs
	Future perspectives
	Acknowledgment
	References
	Further reading
2
Diversity and types of small RNA
	Small regulatory RNAs: Historical milestones
	Classifying endogenous small RNA in plants
		Hairpin sRNA and microRNA
		Natural antisense transcript siRNA
		Secondary and trans-acting siRNA
		Heterochromatic siRNA
	References
3
Biogenesis of small RNA: Molecular pathways and regulatory mechanisms
	DNA-dependent RNA polymerase
	RNA-dependent RNA polymerase
	Dicer
	Argonaute proteins in plants
		Ago1
		Ago10
		Ago5
		Ago7
		AGO2 and AGO3
		Ago4
		Ago6
		AGO8 and AGO9
	Determinants for AGO-sRNA sorting and biological function
	Small RNA in transgenerational epigenetic inheritance
	Interrelationship between sRNA pathways
	Analyzing sRNA: Computational challenges from the “dry lab”
	References
4
Transcriptome-based identification of small RNA in plants: The need for robust prediction algorithms
	Introduction
	The need for small RNA Seq in plants
	Types of RNA Seq strategies
		dUTP-based strand-specific RNA Seq
		Bulked segregant analysis (BSA) using RNA Seq
		Double-stranded RNA Seq
		Differential RNA Seq
	Elements of RNA Seq data and analyses
		Raw read
		Read alignment
		Quantification
		Transcript identification
		Alignment
		Differential gene expression analyses
		Alternative splicing identification
		Identifying gene fusions
	Challenges and solutions for annotating small RNAs in plants
	Empirical toolkits and databases
		Fastx
		miRCat
		SiloCo
		miRBASE
		TAPIR [ http://bioinformatics.psb.ugent.be/webtools/tapir/ ]
	Emerging algorithms
		Validation of expression using time course data
		Normalization and log ratio transformation method
	Tools and databases available according to the basic steps of RNA Seq data analyses
		Quality control
		Trimming and adapters removal
		Error correction
		Bias correction
		Other tasks/preprocessing data
		Alignment tools
		De novo splice aligners
		Normalization, quantitative analysis, and differential expression
		Open (free) source solutions
	Alternative splicing analysis
	Differential isoform/transcript usage
	Fusion genes/chimeras/translocation finders/structural variations
		Single-cell RNA Seq
		Integrated packages
		Genome-guided assemblers [88, 89]
		Co-expression networks
		Visualization tools
		Functional, network, and pathway analysis tools
		Links to databases used for analysis of plant transcriptome data
	A case study: Transcriptome analyses from Vigna mungo and identification of miRNAs
		Background of the work
		Sample preparation and sequencing
		Screening and identification of miRNAs from sequenced data
		Identification of established and novel miRNA sequences
		miRNA target prediction, gene ontology classification, and quantification of target genes
	Quantification of miRNAs in different tissues to study their tissue-specific expression
	Expression patterns of miRNAs from both mock control (MC) and MYMIV-inoculated (MI) datasets
	qPCR validation of miRNA targets in MYMIV-susceptible and -resistant background
	References
	Further reading
Section 2: Expression and regulation mechanism of small RNA
5
Role of RNA interference in seed germination
	Introduction
	Mechanism of seed germination
		Phases in seed germination
		Factors regulating seed germination
	The phenomenon of RNA silencing
		Mechanism of RNA silencing
		miRNAs
		Tasi-RNAs
	Role of small RNAs in seed germination
	miRNA serve as convergence regulatory nodes
	Conclusion
	Acknowledgment
	References
6
Importance of small RNA in plant seed germination
	Brief introduction of seed germination
	miRNAs related to seed germination in Arabidopsis
	miRNAs related to seed germination in crops
	siRNAs related to seed germination
	References
	Further reading
7
Importance of small RNA in plant metabolism
	Introduction
	Major types of plant sRNA
	Biogenesis of small RNA in plants: microRNA and small interference RNA
	Diverse functions of sRNA in controlling plant metabolism during stress condition
	Role of miRNAs in ABA-mediated stress responses
	miRNA-mediated adaptive response to drought and salt stress conditions
	Regulation of cold and heat stress tolerance by miRNAs expression
	miRNAs expression to hypoxia and oxidative stress
	miRNA in response to nutrient homeostasis
	Regulating plant metabolism: Role of sRNAs
		miRNA-mediated regulation plant phytohormone signaling
		miRNA: Transcription factors in regulating plant metabolism
	Functional role of miRNA in plant secondary metabolism biosynthesis
	Regulatory role of siRNAs in plant stress responses
	Conclusion and future prospectus
	References
	Further reading
8
Small RNA in tolerating various biotic stresses
	Small RNA: Discovery, classifications, and biogenesis
		Classification
		MicroRNAs and isomiRs
		Ta-siRNAs
		Nat siRNA
		Heterochromatic-siRNA
		Pathogen-derived sRNAs and miRNA-like molecules
		Biogenesis
	Methodologies applied for sRNA research
	Parameters applied for sRNA prediction
		Plant miRNAs and pathogen milRs
		Plant ta-siRNAs
		Plant isomiRs
	Databases available for sRNAs
	SRNA-mediated biotic stress responses in plants
		SRNA-mediated responses against insects
		SRNA-mediated responses against fungi
		SRNA-mediated responses against virus
		SRNA-mediated responses against bacteria
	SRNA-mediated responses against abiotic stress
	SRNAs and agricultural improvement
	Small RNA as a spray
	Conclusion
	References
	Further reading
9
Role of small RNA in regulating plant viral pathogenesis
	Introduction
	Illustrations of siRNA-mediated and miRNA-mediated antivirus pathway mechanisms
	Role of miRNA in plant antiviral defense
	Application of siRNA against plant antiviral defense
	Regulation of siRNA for plant viral pathogenesis
	siRNA response against bacterial diseases
	Role of siRNA to prevent fungal disease
	References
10
Salt stress tolerance and small RNA
	Introduction
	Plant sRNAs: Types and biogenesis
		miRNA
		siRNA
			Trans-acting siRNAs (ta-siRNAs)
			Natural antisense siRNAs (nat-siRNAs)
			Heterochromatic siRNAs (hec-siRNAs)
	Role of sRNAs in salt stress response
	Conclusion and future perspective
	Acknowledgment
	References
	Further reading
11
Small RNAs and cold stress tolerance
	Introduction
	Cold stress sensing and second messengers
		Mechanism of cold acclimatization
		Small RNAs and cold stress tolerance
	Biogenesis of miRNAs and siRNAs
	Role of miRNAs in cold stress tolerance
	Role of siRNAs in cold stress tolerance
	Genes involved in cold stress
	Conclusion
	References
	Further reading
12
Toward elucidating the functions of miRNAs in drought stress tolerance
	Introduction
	Drought and drought tolerance mechanisms
		Drought escape
		Drought avoidance
		Drought tolerance
		Physiological and biochemical mechanisms of drought tolerance
			Stomatal aperture regulation
			Reactive oxygen species accumulation
			Metabolism maintenance
		Molecular basis of drought tolerance
			Transcription factors
			MiRNAs
				Discovery of miRNAs
				Biogenesis of miRNAs
			Functional modes of miRNAs
		MiRNA responses to drought stress
		Targets of drought-responsive miRNAs
		Contribution of miRNAs to drought stress tolerance
	Conclusion and future perspectives
	References
13
Regulation of photosynthesis and vegetative growth of plants by small RNAs
	Introduction
	Roles of small RNAs in vegetative growth
		Regulation of shoot apical meristem genes
		Abaxial-adaxial polarity
		Morphology and size of leaves
		Guard cell patterning
		Leaf senescence
	Vegetative phase transition
	Regulation of root traits
	Roles of small RNAs in photosynthesis
	Possible applications of small RNAs in modulating photosynthesis and vegetative growth
		Rice
		Tobacco
		Potato
		Maize
		Legume
		Wheat
		Poplar
		Tomato
	Conclusion
	References
14
Heat stress tolerance through small RNA
	Introduction
	Biogenesis
	How do miRNAs regulate stress response?
	Heat-responsive miRNAs in plants
	MiRNA families in cereal crops and their regulatory pathways
		miR156 family
		miR159 family
		miR160 family
		miR164 family
		miR166 family
		miR167 family
		miR168 family
		miR169 family
		miR172 family
		miR319 family
		miR393 family
		miR395 family
		miR397 family
		miR398 family
		miR408 family
	Manipulation of miRNAs for crop improvement
		Target mimics
		Artificial miRNAs
		miRNA manipulation by genome editing technologies
	Conclusion
	Acknowledgment
	References
	Further reading
15
Role of small RNA in plant interaction with microbes
	Introduction
	Structural diversity of sRNAs in plants
		miRNAs
		siRNAs
	miRNAs regulation in response to beneficial microorganism-plant interactions
		MicroRNAs-based regulation in plants submitted to beneficial bacteria
		MicroRNAs-based regulation in plants submitted to beneficial fungi
	sRNAs in response to pathogenic microorganism-plant interactions
		Plant defense strategies
		Counteracting pathogen strategies
	Conclusion and future perspectives
	References
16
Plant growth regulation by small RNA-mediated plant-biotic interactions
	Introduction
	Mode of action of sRNAs in plant defense
	Function of small RNA
		Small RNAs and pathogenesis
			Pathogen-endogenous sRNAs
			Pathogen-induced sRNAs
	Small RNAs and plant defense
		Bacterial infection
		Fungal infection
		Viral infection
	Small RNAs and symbiotic relationships
	Summary
	References
17
Small RNA and DNA methylation in plants
	Brief overview of small RNAs
	Transcriptional gene silencing
	DNA methylation and demethylation
		DNA methylation
		Active DNA demethylation
	Argonaute proteins and their functions
		Argonaute protein family
		Argonaute function in Arabidopsis
	Mobile small RNAs
	Small RNAs and epigenetic reprogramming in plant sexual production
	miRNA and DNA methylation
	A Dicer-independent pathway for biogenesis of siRNAs that direct DNA methylation in Arabidopsis
	sRNA and hybrid vigor
	DNA methylation and fleshy fruit ripening
	Simpson’s paradox on DNA methylation comparison
	Concluding remarks
	Acknowledgments
	References
Section 3: Application of small RNA
18
Small RNA manipulation in plants: Techniques and recent developments
	Introduction
	Small RNA silencing pathways
		MicroRNA (miRNA) pathway
		Small interfering RNA (siRNA) pathway
		Other RNA silencing-related pathways
			Trans-acting siRNA (tasiRNA) pathway
			RdDM pathway in plants
			The natsiRNA pathway
			Exogenic nucleic acid-based RNA silencing
	Recent RNA silencing techniques in plants
		Hairpin RNA transgene (HpRNA)-induced RNA silencing
		Artificial miRNA (amiRNA) technology
			Designing of amiRNAs
		Virus-induced gene silencing (VIGS)
			Different methods of VIGS induction
				Transformation using Agrobacterium tumefaciens
				VIGS for potato silencing through Potato Virus X (PVX)
				VIGS for Arabidopsis silencing through TRV
				TYMV-derived silencing in Arabidopsis
	Applications of RNA interference
		Crop improvement and nutritional value
			RNAi-induced rice and barley
			RNAi induced in banana
			RNAi induced in jute and cotton
		Application of RNAi in biotic stress
		RNAi in secondary metabolite biosynthetic pathway
		RNAi in seedless fruit production
		Application of RNAi developing valuable industrial products
		RNAi to induce prolonged shelf life
		RNAi to silence toxic compounds and allergens in edible fruits
		RNAi for non-hazardous oil production
	Limitations of RNAi
	Biosafety concerns of RNAi technology
	Conclusion
	References
19
MicroRNA-mediated regularity functions under salinity stress in plants
	Introduction: Role of microRNAs in abiotic stresses in plants
	miRNA abundance and dynamics under salinity stress
	Regulation of miRNAs and associated target genes under salt stress
	Development of microRNA-mediated salinity tolerance in plants
	Conclusions and perspectives
	References
20
Biotic stress-tolerant plants through small RNA technology
	Plant biotic stress
	Plant immunity responses against biotic stress factors
	Biotic stress response related to small RNAs
	Role of small RNAs in virus-plant interactions
	Role of small RNAs in bacteria-plant interactions
	Role of small RNAs in fungi-plant interactions
	Role of small RNAs in nematode-plant interactions
	Role of small RNAs in herbivore-plant interactions
	Small RNA applications for biotic resistance
	Artificial miRNA applications
	Site-specific genome editing applications
	References
21
Application of miRNA in fruit quality improvement
	Introduction
	MicroRNA and fruit texture
	MicroRNA and fruit coloration
	MicroRNA and fruit development
	MicroRNA and fruit ripening
	Concluding remarks and future prospects
	References
22
Physiological modification of plants through small RNA
	Foundations of plant physiology
	Regulation of the physiological development
	Discovery of plant small RNAs
		Classification on the basis of RNA source
		Classification on the basis of RNA synthesis
		General mode of action
	Small RNAs in physiological development regulations
		Chromatin modification
		Target degradation
		Lowering translational efficiency
	Small RNA-mediated physiological and developmental control
		Vegetative growth
			Shoot apical meristem development and maintenance
			Leaf development
			Root development
		Phase transition
		Floral development
			Flower patterning
			Flower development
		Seed development, maturation, and germination
			Seed development and trigger for embryo formation
			Seed maturation and storage of products
			Seed size control
			Seed germination
	Conclusions and perspectives
	References
23 Small RNA technology for plant abiotic stress tolerance
	Introduction
	Application of sRNA technology in plants
	General mechanism of RNAi
	The biology of miRNAs in plants
	siRNA-mediated abiotic stress tolerance in plants
	MicroRNA-mediated abiotic stress tolerance in plants
	Conclusion
	References
Section 4: Future scope
24
Challenges of small RNA technology
	Small RNAs in plants: An expanding world
	RNA interference: Basis of small RNA technology
	Small RNA technology: Enormous potential
		Disease resistance
		Metabolic engineering
		Abiotic stress
		Male sterility
	Small RNA technology: Its challenges and pitfalls
		Off-target effects
		Stability of transgene
		Persistence of double-stranded RNAs (dsRNAs)
		Food risk assessment of genetically modified (GM) plants
		Biosafety evaluation of genetically modified (GM) plants
	Future prospects
		Bioinformatics approaches to achieve better gene silencing
		Spray-induced gene silencing
		CRISPR/Cas9: A platform for editing plant genomes
	Conclusions
	References
25
Future scope of small RNA technology in crop science
	Introduction
	Overview of diverse small RNA pathways in plants
	Perspectives on small RNA sequencing and trafficking
	Developments and challenges of sRNA-mediated gene silencing for crop improvement
	Stress memory and forgetfulness in plants
	Small RNA-mediated epigenetic engineering and RNA editing in plants
	Small RNA trafficking between kingdoms and applications for plant disease control
	Conclusion
	Acknowledgments
	References
Index
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