RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants.

Abstract:

:RNA-directed DNA methylation (RdDM) is an epigenetic process in plants that involves both short and long noncoding RNAs. The generation of these RNAs and the induction of RdDM rely on complex transcriptional machineries comprising two plant-specific, RNA polymerase II (Pol II)-related RNA polymerases known as Pol IV and Pol V, as well as a host of auxiliary factors that include both novel and refashioned proteins. We present current views on the mechanism of RdDM with a focus on evolutionary innovations that occurred during the transition from a Pol II transcriptional pathway, which produces mRNA precursors and numerous noncoding RNAs, to the Pol IV and Pol V pathways, which are specialized for RdDM and gene silencing. We describe recently recognized deviations from the canonical RdDM pathway, discuss unresolved issues, and speculate on the biological significance of RdDM for flowering plants, which have a highly developed Pol V pathway.

journal_name

Annu Rev Plant Biol

authors

Matzke MA,Kanno T,Matzke AJ

doi

10.1146/annurev-arplant-043014-114633

subject

Has Abstract

pub_date

2015-01-01 00:00:00

pages

243-67

eissn

1543-5008

issn

1545-2123

journal_volume

66

pub_type

杂志文章,评审
  • Global studies of cell type-specific gene expression in plants.

    abstract::Technological advances in expression profiling and in the ability to collect minute quantities of tissues have come together to allow a growing number of global transcriptional studies at the cell level in plants. Microarray technology, with a choice of cDNA or oligo-based slides, is now well established, with commerc...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.57.032905.105302

    authors: Galbraith DW,Birnbaum K

    更新日期:2006-01-01 00:00:00

  • Plant immunity to insect herbivores.

    abstract::Herbivorous insects use diverse feeding strategies to obtain nutrients from their host plants. Rather than acting as passive victims in these interactions, plants respond to herbivory with the production of toxins and defensive proteins that target physiological processes in the insect. Herbivore-challenged plants als...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.59.032607.092825

    authors: Howe GA,Jander G

    更新日期:2008-01-01 00:00:00

  • MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions.

    abstract::MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced sile...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-050718-100334

    authors: Song X,Li Y,Cao X,Qi Y

    更新日期:2019-04-29 00:00:00

  • The Structural Basis of Ligand Perception and Signal Activation by Receptor Kinases.

    abstract::Plants have evolved a family of unique membrane receptor kinases to orchestrate the growth and development of their cells, tissues, and organs. Receptor kinases also form the first line of defense of the plant immune system and allow plants to engage in symbiotic interactions. Here, we discuss recent advances in under...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-042916-040957

    authors: Hohmann U,Lau K,Hothorn M

    更新日期:2017-04-28 00:00:00

  • Genomics, Physiology, and Molecular Breeding Approaches for Improving Salt Tolerance.

    abstract::Salt stress reduces land and water productivity and contributes to poverty and food insecurity. Increased salinization caused by human practices and climate change is progressively reducing agriculture productivity despite escalating calls for more food. Plant responses to salt stress are well understood, involving nu...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-042916-040936

    authors: Ismail AM,Horie T

    更新日期:2017-04-28 00:00:00

  • Genetic Regulation of Shoot Architecture.

    abstract::Shoot architecture is determined by the organization and activities of apical, axillary, intercalary, secondary, and inflorescence meristems and by the subsequent development of stems, leaves, shoot branches, and inflorescences. In this review, we discuss the unifying principles of hormonal and genetic control of shoo...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-042817-040422

    authors: Wang B,Smith SM,Li J

    更新日期:2018-04-29 00:00:00

  • The Costs of Photorespiration to Food Production Now and in the Future.

    abstract::Photorespiration is essential for C3 plants but operates at the massive expense of fixed carbon dioxide and energy. Photorespiration is initiated when the initial enzyme of photosynthesis, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), reacts with oxygen instead of carbon dioxide and produces a toxic compo...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-043015-111709

    authors: Walker BJ,VanLoocke A,Bernacchi CJ,Ort DR

    更新日期:2016-04-29 00:00:00

  • Genetic regulation of time to flower in Arabidopsis thaliana.

    abstract::In Arabidopsis thaliana, the initiation of flowering is carried out by four genetic pathways: gibberellin, autonomous, vernalization, and light-dependent pathways. These processes are integrated by the function of the genes FD, FE, FWA, PDF2, SOC1, and FT at the integration pathway. The integrated signal of the floral...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.55.031903.141644

    authors: Komeda Y

    更新日期:2004-01-01 00:00:00

  • Fruit development and ripening.

    abstract::Fruiting structures in the angiosperms range from completely dry to highly fleshy organs and provide many of our major crop products, including grains. In the model plant Arabidopsis, which has dry fruits, a high-level regulatory network of transcription factors controlling fruit development has been revealed. Studies...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-050312-120057

    authors: Seymour GB,Østergaard L,Chapman NH,Knapp S,Martin C

    更新日期:2013-01-01 00:00:00

  • The complex fate of alpha-ketoacids.

    abstract::Plant cells are unique in that they contain four species of alpha-ketoacid dehydrogenase complex: plastidial pyruvate dehydrogenase, mitochondrial pyruvate dehydrogenase, alpha-ketoglutarate (2-oxoglutarate) dehydrogenase, and branched-chain alpha-ketoacid dehydrogenase. All complexes include multiple copies of three ...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.53.100301.135251

    authors: Mooney BP,Miernyk JA,Randall DD

    更新日期:2002-01-01 00:00:00

  • The Small GTPase Superfamily in Plants: A Conserved Regulatory Module with Novel Functions.

    abstract::Small GTP-binding proteins represent a highly conserved signaling module in eukaryotes that regulates diverse cellular processes such as signal transduction, cytoskeletal organization and cell polarity, cell proliferation and differentiation, intracellular membrane trafficking and transport vesicle formation, and nucl...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-112619-025827

    authors: Nielsen E

    更新日期:2020-04-29 00:00:00

  • Photoreceptor signaling networks in plant responses to shade.

    abstract::The dynamic light environment of vegetation canopies is perceived by phytochromes, cryptochromes, phototropins, and UV RESISTANCE LOCUS 8 (UVR8). These receptors control avoidance responses to preclude exposure to limiting or excessive light and acclimation responses to cope with conditions that cannot be avoided. The...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-050312-120221

    authors: Casal JJ

    更新日期:2013-01-01 00:00:00

  • Mechanisms of salinity tolerance.

    abstract::The physiological and molecular mechanisms of tolerance to osmotic and ionic components of salinity stress are reviewed at the cellular, organ, and whole-plant level. Plant growth responds to salinity in two phases: a rapid, osmotic phase that inhibits growth of young leaves, and a slower, ionic phase that accelerates...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.59.032607.092911

    authors: Munns R,Tester M

    更新日期:2008-01-01 00:00:00

  • 14-3-3 and FHA domains mediate phosphoprotein interactions.

    abstract::Many aspects of plant growth and development require specific protein interactions to carry out biochemical and cellular functions. Several proteins mediate these interactions, two of which specifically recognize phosphoproteins: 14-3-3 proteins and proteins with FHA domains. These are the only phosphobinding domains ...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.59.032607.092844

    authors: Chevalier D,Morris ER,Walker JC

    更新日期:2009-01-01 00:00:00

  • Cryptochrome structure and signal transduction.

    abstract::Cryptochromes are photosensory receptors mediating light regulation of growth and development in plants. Since the isolation of the Arabidopsis CRY1 gene in 1993, cryptochromes have been found in every multicellular eukaryote examined. Most plant cryptochromes have a chromophore-binding domain that shares similar stru...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.54.110901.160901

    authors: Lin C,Shalitin D

    更新日期:2003-01-01 00:00:00

  • Adventitious roots and lateral roots: similarities and differences.

    abstract::In addition to its role in water and nutrient uptake, the root system is fundamentally important because it anchors a plant to its substrate. Although a wide variety of root systems exist across different species, all plants have a primary root (derived from an embryonic radicle) and different types of lateral roots. ...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-050213-035645

    authors: Bellini C,Pacurar DI,Perrone I

    更新日期:2014-01-01 00:00:00

  • Laser microdissection of plant tissue: what you see is what you get.

    abstract::Laser microdissection (LM) utilizes a cutting or harvesting laser to isolate specific cells from histological sections; the process is guided by microscopy. This provides a means of removing selected cells from complex tissues, based only on their identification by microscopic appearance, location, or staining propert...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.56.032604.144138

    authors: Nelson T,Tausta SL,Gandotra N,Liu T

    更新日期:2006-01-01 00:00:00

  • Algal sensory photoreceptors.

    abstract::Only five major types of sensory photoreceptors (BLUF-proteins, cryptochromes, phototropins, phytochromes, and rhodopsins) are used in nature to regulate developmental processes, photosynthesis, photoorientation, and control of the circadian clock. Sensory photoreceptors of algae and protists are exceptionally rich in...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.59.032607.092847

    authors: Hegemann P

    更新日期:2008-01-01 00:00:00

  • Classification and comparison of small RNAs from plants.

    abstract::Regulatory small RNAs, which range in size from 20 to 24 nucleotides, are ubiquitous components of endogenous plant transcriptomes, as well as common responses to exogenous viral infections and introduced double-stranded RNA (dsRNA). Endogenous small RNAs derive from the processing of helical RNA precursors and can be...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-050312-120043

    authors: Axtell MJ

    更新日期:2013-01-01 00:00:00

  • Tapping the promise of genomics in species with complex, nonmodel genomes.

    abstract::Genomics is enabling a renaissance in all disciplines of plant biology. However, many plant genomes are complex and remain recalcitrant to current genomic technologies. The complexities of these nonmodel plant genomes are attributable to gene and genome duplication, heterozygosity, ploidy, and/or repetitive sequences....

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-050312-120237

    authors: Hirsch CN,Buell CR

    更新日期:2013-01-01 00:00:00

  • Preadaptation and Naturalization of Nonnative Species: Darwin's Two Fundamental Insights into Species Invasion.

    abstract::Predicting which nonnative species become invasive is critical for their successful management, and Charles Darwin provided predictions based on species' relatedness. However, Darwin provided two opposing predictions about the relatedness of introduced nonnatives to indigenous species. First, environmental fit is the ...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-042817-040339

    authors: Cadotte MW,Campbell SE,Li SP,Sodhi DS,Mandrak NE

    更新日期:2018-04-29 00:00:00

  • Plant nitrogen assimilation and use efficiency.

    abstract::Crop productivity relies heavily on nitrogen (N) fertilization. Production and application of N fertilizers consume huge amounts of energy, and excess is detrimental to the environment; therefore, increasing plant N use efficiency (NUE) is essential for the development of sustainable agriculture. Plant NUE is inherent...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-042811-105532

    authors: Xu G,Fan X,Miller AJ

    更新日期:2012-01-01 00:00:00

  • High-throughput characterization of plant gene functions by using gain-of-function technology.

    abstract::Gain-of-function approaches have been used as an alternative or complementary method to loss-of-function approaches as well as to confer new functions to plants. Gain-of-function is achieved by increasing gene expression levels through the random activation of endogenous genes by transcriptional enhancers or the expre...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-042809-112143

    authors: Kondou Y,Higuchi M,Matsui M

    更新日期:2010-01-01 00:00:00

  • Chloroplast RNA metabolism.

    abstract::The chloroplast genome encodes proteins required for photosynthesis, gene expression, and other essential organellar functions. Derived from a cyanobacterial ancestor, the chloroplast combines prokaryotic and eukaryotic features of gene expression and is regulated by many nucleus-encoded proteins. This review covers f...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev-arplant-042809-112242

    authors: Stern DB,Goldschmidt-Clermont M,Hanson MR

    更新日期:2010-01-01 00:00:00

  • Alkaloid biosynthesis: metabolism and trafficking.

    abstract::Alkaloids represent a highly diverse group of compounds that are related only by the occurrence of a nitrogen atom in a heterocyclic ring. Plants are estimated to produce approximately 12,000 different alkaloids, which can be organized into groups according to their carbon skeletal structures. Alkaloid biosynthesis in...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.59.032607.092730

    authors: Ziegler J,Facchini PJ

    更新日期:2008-01-01 00:00:00

  • The plant heterotrimeric G-protein complex.

    abstract::Heterotrimeric G-protein complexes couple extracellular signals via cell surface receptors to downstream enzymes called effectors. Heterotrimeric G-protein complexes, together with their cognate receptors and effectors, operate at the apex of signal transduction. In plants, the number of G-protein complex components i...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.58.032806.103827

    authors: Temple BR,Jones AM

    更新日期:2007-01-01 00:00:00

  • Abscission, dehiscence, and other cell separation processes.

    abstract::Cell separation is a critical process that takes place throughout the life cycle of a plant. It enables roots to emerge from germinating seeds, cotyledons, and leaves to expand, anthers to dehisce, fruit to ripen, and organs to be shed. The focus of this review is to examine how processes such as abscission and dehisc...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.53.092701.180236

    authors: Roberts JA,Elliott KA,Gonzalez-Carranza ZH

    更新日期:2002-01-01 00:00:00

  • A genetic regulatory network in the development of trichomes and root hairs.

    abstract::Trichomes and root hairs differentiate from epidermal cells in the aerial tissues and roots, respectively. Because trichomes and root hairs are easily accessible, particularly in the model plant Arabidopsis, their development has become a well-studied model of cell differentiation and growth. Molecular genetic analyse...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.59.032607.092949

    authors: Ishida T,Kurata T,Okada K,Wada T

    更新日期:2008-01-01 00:00:00

  • From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule.

    abstract::Plants, green algae, and cyanobacteria synthesize storage polysaccharides by a similar ADPglucose-based pathway. Plant starch metabolism can be distinguished from that of bacterial glycogen by the presence of multiple forms of enzyme activities for each step of the pathway. This multiplicity does not coincide with any...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章,评审

    doi:10.1146/annurev.arplant.54.031902.134927

    authors: Ball SG,Morell MK

    更新日期:2003-01-01 00:00:00

  • Genetic Engineering and Editing of Plants: An Analysis of New and Persisting Questions.

    abstract::Genetic engineering is a molecular biology technique that enables a gene or genes to be inserted into a plant's genome. The first genetically engineered plants were grown commercially in 1996, and the most common genetically engineered traits are herbicide and insect resistance. Questions and concerns have been raised...

    journal_title:Annual review of plant biology

    pub_type: 杂志文章

    doi:10.1146/annurev-arplant-081519-035916

    authors: Mackelprang R,Lemaux PG

    更新日期:2020-04-29 00:00:00