4.7 Review

Expansion and contraction of small RNA and methylation machinery throughout plant evolution

Related references

Note: Only part of the references are listed.
Article Plant Sciences

Origin, evolution and diversification of plant ARGONAUTE proteins

Zancong Li et al.

Summary: Argonaute (AGO) proteins are essential for RNA interference in eukaryotes, regulating biological processes by silencing target genes through association with small RNAs. A comprehensive phylogenetic analysis identified multiple AGO proteins in 244 plant species, revealing the evolutionary history of the plant AGO family and their roles as RNAi effectors. This study provides insights into the expansion and diversification of AGO proteins in plants, shedding light on their functional roles in different biological processes.

PLANT JOURNAL (2022)

Letter Plant Sciences

Asymmetric expression of Argonautes in reproductive tissues

P. E. Jullien et al.

PLANT PHYSIOLOGY (2022)

Article Biology

A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation

Andrew Loffer et al.

Summary: Researchers have found that selfish genetic elements in plants are silenced by RNA-directed DNA methylation. The process involves specific RNA molecules and enzymes, which collectively influence the production of siRNAs and ensure maximal siRNA coverage at methylated target loci.

ELIFE (2022)

Article Plant Sciences

CHH DNA methylation increases at 24-PHAS loci depend on 24-nt phased small interfering RNAs in maize meiotic anthers

Mei Zhang et al.

Summary: In maize, the 24-nt phasiRNAs are essential for targeting increased DNA methylation at specific loci in anthers, and not just for transcriptional activation of PHAS precursors. Mutants of male sterile23 and Dicer-like5 genes lack sufficient 24-nt phasiRNAs, showing the importance of these small RNA molecules in regulating male fertility.

NEW PHYTOLOGIST (2021)

Article Multidisciplinary Sciences

Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation

Qian Wang et al.

Summary: In plants, DICER-LIKE PROTEIN 3 (DCL3) produces 24-nucleotide (nt) small interfering RNAs (siRNAs) that determine the specificity of the RNA-directed DNA methylation pathway. The structure and functional mechanisms of DCL3 in this process provide insight into the RNA-directed DNA methylation pathway in plants.

SCIENCE (2021)

Article Multidisciplinary Sciences

Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA

Kun Huang et al.

Summary: DNA methylation plays a crucial role in gene expression and genome integrity in plants. The complex formed by Pol IV and RDR2 is involved in dsRNA synthesis, revealing a mechanism of "backtracking-triggered RNA channeling".

SCIENCE (2021)

Article Biology

Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes

Sibo Wang et al.

Summary: The study reveals that streptophyte algae progressively adapted to a subaerial environment through the evolution of plant-like miRNA biosynthesis and degradation pathways. Two major evolutionary transitions in small RNA metabolism in streptophyte algae were identified, linked to abiotic stress responses, evolution of multicellularity, pathogen defense, and antibacterial immunity. The origin and diversification of DICER and AGO genes among streptophyte algae reflected progressive adaptations during evolution.

COMMUNICATIONS BIOLOGY (2021)

Article Multidisciplinary Sciences

The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice

Kezhi Zheng et al.

Summary: This study reveals the essential role of rice Pol V in CHH methylation on RdDM loci, as well as its impact on the production and accumulation of 24-nt siRNAs. Pol V functions on loci with high CHH methylation levels and low CG and CHG methylation levels, while being not required on other loci.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Plant Sciences

Reproductive phasiRNA loci and DICER-LIKE5, but not microRNA loci, diversified in monocotyledonous plants

Parth Patel et al.

Summary: Sequencing of sRNAs from 28 phylogenetically diverse monocots and early-diverging angiosperm lineages revealed differences in miRNA content between grasses and other monocot families. A curated miRNA database was used to identify conservation at specific positions, hypothesized to be signatures of selection. This study provides insights into sRNA diversity in flowering plants and the origins of important phasiRNA biogenesis genes in grasses.

PLANT PHYSIOLOGY (2021)

Review Biochemistry & Molecular Biology

Evolution of DNA Methylome Diversity in Eukaryotes

Alex de Mendoza et al.

JOURNAL OF MOLECULAR BIOLOGY (2020)

Article Biochemistry & Molecular Biology

The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants

Chen Jiao et al.

Article Biochemistry & Molecular Biology

Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants

Alice Lunardon et al.

GENOME RESEARCH (2020)

Article Multidisciplinary Sciences

Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize

Chong Teng et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

DNA methylation mutants in Physcomitrella patens elucidate individual roles of CG and non-CG methylation in genome regulation

Katherine Domb et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Plant Sciences

DNA methylation in Marchantia polymorpha

Adolfo Aguilar-Cruz et al.

NEW PHYTOLOGIST (2019)

Article Multidisciplinary Sciences

24-nt reproductive phasiRNAs are broadly present in angiosperms

Rui Xia et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs

Rafael Yaari et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela

Dong An et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biotechnology & Applied Microbiology

Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce

Miyuki Nakamura et al.

BMC GENOMICS (2019)

Review Cell Biology

Dynamics and function of DNA methylation in plants

Huiming Zhang et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)

Review Plant Sciences

Plant evolution: landmarks on the path to terrestrial life

Jan de Vries et al.

NEW PHYTOLOGIST (2018)

Article Biochemistry & Molecular Biology

Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops

Joshua T. Trujillo et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biotechnology & Applied Microbiology

Conservation and divergence of small RNA pathways and microRNAs in land plants

Chenjiang You et al.

GENOME BIOLOGY (2017)

Article Biotechnology & Applied Microbiology

The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants

Adam J. Bewick et al.

GENOME BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Taiji Kawakatsu et al.

Article Cell Biology

Evidence for ARGONAUTE4-DNA interactions in RNA-directed DNA methylation in plants

Sylvie Lahmy et al.

GENES & DEVELOPMENT (2016)

Article Multidisciplinary Sciences

DNA methylome of the 20-gigabase Norway spruce genome

Israel Ausin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Plant Sciences

Charophytes: Evolutionary Giants and Emerging Model Organisms

David S. Domozych et al.

FRONTIERS IN PLANT SCIENCE (2016)

Article Biotechnology & Applied Microbiology

Widespread natural variation of DNA methylation within angiosperms

Chad E. Niederhuth et al.

GENOME BIOLOGY (2016)

Article Biochemistry & Molecular Biology

A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis

Jixian Zhai et al.

Review Plant Sciences

Evolution, functions, and mysteries of plant ARGONAUTE proteins

Han Zhang et al.

CURRENT OPINION IN PLANT BIOLOGY (2015)

Review Plant Sciences

RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules

Ming Zhou et al.

CURRENT OPINION IN PLANT BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Ancient Origin and Recent Innovations of RNA Polymerase IV and V

Yi Huang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Review Cell Biology

The expanding world of small RNAs in plants

Filipe Borges et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Article Multidisciplinary Sciences

Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers

Jixian Zhai et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemistry & Molecular Biology

ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation

Andrea D. McCue et al.

EMBO JOURNAL (2015)

Review Genetics & Heredity

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

Marjori A. Matzke et al.

NATURE REVIEWS GENETICS (2014)

Article Biochemistry & Molecular Biology

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

Hume Stroud et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)

Article Multidisciplinary Sciences

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

Patrick T. West et al.

PLOS ONE (2014)

Article Multidisciplinary Sciences

Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

Liya Wei et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

The Norway spruce genome sequence and conifer genome evolution

Bjorn Nystedt et al.

NATURE (2013)

Article Multidisciplinary Sciences

Broad Phylogenomic Sampling and the Sister Lineage of Land Plants

Ruth E. Timme et al.

PLOS ONE (2012)

Article Genetics & Heredity

A Functional Phylogenomic View of the Seed Plants

Ernest K. Lee et al.

PLOS GENETICS (2011)

Article Multidisciplinary Sciences

Control of female gamete formation by a small RNA pathway in Arabidopsis

Vianey Olmedo-Monfil et al.

NATURE (2010)

Article Biochemistry & Molecular Biology

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

Cameron Johnson et al.

GENOME RESEARCH (2009)

Article Biochemistry & Molecular Biology

A multistep process gave rise to RNA polymerase IV of land plants

Jie Luo et al.

JOURNAL OF MOLECULAR EVOLUTION (2007)

Article Biochemistry & Molecular Biology

Low temperature inhibits RNA silencing-mediated defence by the control of siRNA generation

G Szittya et al.

EMBO JOURNAL (2003)