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| Open AccessPhytochrome B photobodies are comprised of phytochrome B and its primary and secondary interacting proteins
Phytochrome is a photoreceptor forming a membraneless organelle called a photobody. The authors isolated the photobody and found that the photobody is made of not only phytochrome but also its primary and secondary interacting proteins.
- Chanhee Kim
- , Yongmin Kwon
- & Giltsu Choi
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Article
| Open AccessDistinct roles of Arabidopsis ORC1 proteins in DNA replication and heterochromatic H3K27me1 deposition
The dynamics of DNA replication factors is crucial for cell cycle progression. Arabidopsis encode two origin recognition complex 1 proteins, ORC1a and ORC1b, with distinct roles in DNA replication and deposition of heterochromatic H3K27me1, respectively.
- Zaida Vergara
- , María S. Gomez
- & Crisanto Gutierrez
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| Open AccessThe Arabidopsis endosperm is a temperature-sensing tissue that implements seed thermoinhibition through phyB
Piskurewicz et al. show that seed thermoinhibition is controlled by endospermic phytochrome B (phyB). High temperature decreases endospermic phyB signaling, which promotes DELLA- and PIFmediated endospermic ABA release that blocks germination.
- Urszula Piskurewicz
- , Maria Sentandreu
- & Luis Lopez-Molina
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Article
| Open AccessHistone H2A monoubiquitination marks are targeted to specific sites by cohesin subunits in Arabidopsis
How histone H2A monoubiquitination (H2Aub1) is established at specific genomic locations remains unclear. Here, the authors report that Arabidopsis cohesin subunits SCC3 and SYN4 are involved in H2Aub1 through their direct or indirect interaction with BMI1A/B/C subunits of PRC1, the E3 ligases in PRC1 for H2Aub1.
- Yu Zhang
- , Min Ma
- & Yuda Fang
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Article
| Open AccessHSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions
Here the authors show genome-wide chromatin changes and transcriptional reprogramming occur in response to heat stress in tomato, leading to the transient formation of promoter-enhancer contacts to drive the expression of heat-stress responsive genes. Furthermore, they show chromatin spatial reorganization requires HSFA1a, a transcription factor (TF) essential for heat stress tolerance in tomato.
- Ying Huang
- , Jing An
- & Moussa Benhamed
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Article
| Open AccessComplementary peptides represent a credible alternative to agrochemicals by activating translation of targeted proteins
Feeding an increasing world population in the context of climate change is one of the grand challenges faced by our generation. Here, the authors show that external application of synthetic complementary peptides can increase the abundance of target proteins to modulate plant growth or stress resistance.
- Mélanie Ormancey
- , Bruno Guillotin
- & Jean-Philippe Combier
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| Open AccessPollen tube emergence is mediated by ovary-expressed ALCATRAZ in cucumber
Pollen tube growth is guided towards ovules. Here the authors show that a bHLH transcriptional factor CsALC functions in pollen tube emergence towards ovules to regulate female fertility in cucumber and promotes the expression of two rapid alkalinization factors CsRALF4/19 in the ovary.
- Zhihua Cheng
- , Xiaofeng Liu
- & Xiaolan Zhang
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Article
| Open AccessArabidopsis DXO1 activates RNMT1 to methylate the mRNA guanosine cap
Arabidopsis DXO1 is a member of the eukaryotic DXO family of decapping enzymes for NAD-capped RNAs. Here the authors show that DXO1 is an essential component in canonical m7G capping of mRNA and activates RNMT1 which methylates the guanosine cap to form the m7G cap.
- Chen Xiao
- , Kaien Li
- & Yiji Xia
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Article
| Open AccessImproving cassava bacterial blight resistance by editing the epigenome
Activating the expression of host susceptibility (S) genes is one of the strategies plant pathogens employed to promote infection of their host. Here, the authors show that targeted methylation at the TAL20 effector binding element of the cassava SWEET10a gene lead to resistance to Xanthomonas phaseoli.
- Kira M. Veley
- , Kiona Elliott
- & Rebecca S. Bart
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| Open AccessArabidopsis γ-H2A.X-INTERACTING PROTEIN participates in DNA damage response and safeguards chromatin stability
γ-H2A.X is a critical signal for DNA double strand break responses. In this study, an Arabidopsis protein that interacts with γ-H2A.X and the recombinase RAD51 is shown to contribute to plant chromatin stability and integrity.
- Tianyi Fan
- , Huijia Kang
- & Yan Zhu
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Article
| Open AccessBioenergetics of pollen tube growth in Arabidopsis thaliana revealed by ratiometric genetically encoded biosensors
Pollen tube growth involves coordinated energy fluxes between plastids, the cytosol, and mitochondria. Here using ratiometric biosensors, the authors delineate energy flux in growing Arabidopsis pollen tubes by monitoring ATP, NADPH and the NADH/NAD + ratio at the subcellular level.
- Jinhong Liu
- , Shey-Li Lim
- & Boon Leong Lim
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Article
| Open AccessHistone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis
Histone chaperones and chromatin remodelers control nucleosome dynamics. Here the authors show that the Arabidopsis ASF1 chaperone primarily supplies histone variants to the HIRA complex to ensure proper epigenetic gene regulation.
- Zhenhui Zhong
- , Yafei Wang
- & Steven E. Jacobsen
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Article
| Open AccessRNA G-quadruplex structure contributes to cold adaptation in plants
During evolution, plants have adapted to habitats with distinct temperature ranges. In this study, scientists report that a specific RNA structure motif, RNA G-quadruplex (RG4) is enriched across genomes of plant species growing in colder climates.
- Xiaofei Yang
- , Haopeng Yu
- & Yiliang Ding
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Article
| Open AccessExpression strategies for the efficient synthesis of antimicrobial peptides in plastids
Antimicrobial peptides (AMPs) are promising next-generation antibiotics, but are difficult to produce due to the toxicity to bacterial hosts. Here, the authors report the utilization of transplastomic tobacco plants for AMPs production without cytotoxic effects via inducible expression systems and fusions to cleavable carrier protein.
- Matthijs P. Hoelscher
- , Joachim Forner
- & Ralph Bock
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| Open AccessA NAC-EXPANSIN module enhances maize kernel size by controlling nucellus elimination
Current studies of maize kernel development mostly focus on endosperm and embryo development, and little is known about the control of the nucellus tissue. Here, the authors report a NAC-EXPB15 pathway that regulate maize kernel size by modulating nucellus elimination and early endosperm development.
- Qin Sun
- , Yunfu Li
- & Fazhan Qiu
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Article
| Open AccessA fungal tolerance trait and selective inhibitors proffer HMG-CoA reductase as a herbicide mode-of-action
Managing herbicide resistance problem needs the identification of new herbicidal modes of action. Here, the authors solve the crystal structures of Arabidopsis HMGR and show HMGR as a potential new herbicide target by identifying plant-specific HMGR inhibitors and engineering tolerant trait in Arabidopsis.
- Joel Haywood
- , Karen J. Breese
- & Joshua S. Mylne
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Article
| Open AccessVAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC
Cold-induced silencing of Arabidopsis FLC requires the binding of VAL1 to an intronic motif. Here, the authors show that ASAP and PRC1, two interacting partner complexes of VAL1, mediate co-transcriptional repression and chromatin modulation to effectively co-ordinate different steps in FLC silencing.
- Pawel Mikulski
- , Philip Wolff
- & Caroline Dean
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Article
| Open AccessNODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis
Arabidopsis NDX was previously reported as a regulator of euchromatic gene expression. Here the authors show that NDX functions at pericentromeric regions and regulates heterochromatin homeostasis by controlling siRNA production and non-CG methylation.
- Zsolt Karányi
- , Ágnes Mosolygó-L
- & Lóránt Székvölgyi
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| Open AccessStrigolactones are chemoattractants for host tropism in Orobanchaceae parasitic plants
Parasitic plants are able to grow towards potential hosts. Here the authors show that strigolactones produced by the host plants can act as chemoattractants for the root parasites Phtheirospermum japonicum and Striga hermonthica.
- Satoshi Ogawa
- , Songkui Cui
- & Ken Shirasu
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Article
| Open AccessTranscription-coupled and epigenome-encoded mechanisms direct H3K4 methylation
Methylation of histone H3 lysine 4 is associated with transcription. Here the authors describe three Arabidopsis methyltransferases that direct H3K4me1 and propose that one methyltransferase works co-transcriptionally while the others are recruited to genomic and epigenomic features.
- Satoyo Oya
- , Mayumi Takahashi
- & Soichi Inagaki
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Article
| Open AccessMet1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains
Deubiquitinases (DUBs) targeting Met1-linked ubiquitin chains have important functions in mammals but are barely studied in plants. Here, the authors identify rice OTUB1 as a Met1-targeting DUB, characterize the structural determinants of this activity, and show that these features are conserved in green plants.
- Lining Lu
- , Xiaoguo Zhai
- & Feng Wang
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Article
| Open AccessChIP-Hub provides an integrative platform for exploring plant regulome
A comprehensive data portal to explore plant regulomes is still unavailable. Here, the authors develop a web-based platform ChIP-Hub in the ENCODE standards and demonstrate its applications in the identification of hierarchical regulatory network, tissue-specific chromatin dynamics, putative enhancers and chromatin states.
- Liang-Yu Fu
- , Tao Zhu
- & Dijun Chen
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Article
| Open AccessA 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
Single-cell transcriptomics allows gene expression heterogeneity to be assessed at cellular resolution but the original location of each cell is unknown. Here the authors combine single nuclei RNA-seq with 3D spatial reconstruction of floral meristems to link gene activities with morphology.
- Manuel Neumann
- , Xiaocai Xu
- & Jose M. Muino
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| Open AccessA natural allele of OsMS1 responds to temperature changes and confers thermosensitive genic male sterility
Thermosensitive genic male-sterile (TGMS) lines are widely used for two-line hybrid rice breeding, but the mechanism of TGMS has not been fully elucidated. Here, the authors show that natural allele of the OsMS1 gene, encoding a histone binding PHD finger protein, responds to temperature change and confers TGMS in rice.
- Lunying Wu
- , Xiaohui Jing
- & Yunhai Li
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Article
| Open AccessA hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis
Cell division and expansion are carefully coordinated during organ growth. Here, the authors show that the SCL28 and SMOS1 transcription factors interact to regulate cyclin-dependent kinase inhibitors and promote cell size increase over division in Arabidopsis.
- Yuji Nomoto
- , Hirotomo Takatsuka
- & Masaki Ito
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| Open AccessNew recognition specificity in a plant immune receptor by molecular engineering of its integrated domain
Plant NLR proteins trigger immune responses upon recognition of pathogen effectors. Here the authors show that the integrated decoy domain of the rice NLR RGA5 can be engineered to trigger immune responses upon binding a non-cognate effector.
- Stella Cesari
- , Yuxuan Xi
- & Thomas Kroj
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Article
| Open AccessA peroxisomal heterodimeric enzyme is involved in benzaldehyde synthesis in plants
Benzaldehyde is a simple aromatic aldehyde that attracts pollinators, has antifungal properties and contributes to flavor in many plants. Here the authors show that benzaldehyde is synthesized in petunia via the benzoic acid β-oxidative pathway by a peroxisomal heterodimeric enzyme consisting of α and β subunits.
- Xing-Qi Huang
- , Renqiuguo Li
- & Natalia Dudareva
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Article
| Open AccessApoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature
Arabidopsis root hair growth is enhanced at low temperatures. Here the authors show that the class III peroxidases PRX62 and PRX69 modulate ROS homeostasis and cell wall characteristics, and promote root hair elongation at low temperature.
- Javier Martínez Pacheco
- , Philippe Ranocha
- & José M. Estevez
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Article
| Open AccessArabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading
MicroRNAs regulate gene expression through RNA cleavage or translation repression. Here the authors show that RBV, an evolutionarily conserved WD40 domain protein, acts to promote MIR transcription, pri-miRNA processing and miRNA loading into AGO1.
- Chao Liang
- , Qiang Cai
- & Xuemei Chen
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Article
| Open AccessTwo zinc finger proteins with functions in m6A writing interact with HAKAI
The components of m6A writer and their interactions are still far from fully understood. Here, the authors identify two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, as components of the Arabidopsis m6A writer complex, and show that hiz2 mutant plants have an 85% reduction in m6A abundance and severe developmental defects.
- Mi Zhang
- , Zsuzsanna Bodi
- & Rupert G. Fray
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Article
| Open AccessNatural variation in Glume Coverage 1 causes naked grains in sorghum
Low glume coverage is the preferred for easy threshing in grain production, but the genetic basis remains unclear. Here, the authors report the gene GC1, which encodes an atypical G protein γ subunit, negatively regulates sorghum glume coverage and the naturally truncated alleles can be useful in the naked grain breeding.
- Peng Xie
- , Sanyuan Tang
- & Qi Xie
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Article
| Open AccessLocal and global crosstalk among heterochromatin marks drives DNA methylome patterning in Arabidopsis
In plant genomes, both mCG and H3K9me2/mCH are important for silencing transposable elements (TEs). Here, the authors show that establishment of mCH is abolished in both TE and active genes when mCG is lost and targeting efficiency of mCH depends on relative levels of mCG within the genome.
- Taiko Kim To
- , Chikae Yamasaki
- & Tetsuji Kakutani
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| Open AccessGeminiviruses employ host DNA glycosylases to subvert DNA methylation-mediated defense
Plants tightly regulate DNA methylation to regulate gene expression. Here, the authors show that the tomato yellow leaf curl China virus βC1 protein interacts with plant DNA glycosylases to promote demethylation of viral DNA and promote virulence.
- Xiaojian Gui
- , Chang Liu
- & Xueping Zhou
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| Open AccessActivation of the plant mevalonate pathway by extracellular ATP
Products of the mevalonate pathway support plant development. Here the authors show that the extracellular ATP receptor P2K1 phosphorylates mevalonate kinase and this affects the mevalonate pathway.
- Sung-Hwan Cho
- , Katalin Tóth
- & Gary Stacey
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Article
| Open AccessNuA4 and H2A.Z control environmental responses and autotrophic growth in Arabidopsis
Function of nucleosomal acetyltransferase of H4 (NuA4), one major complex of HAT, remains unclear in plants. Here, the authors generate mutants targeting two components of the putative NuA4 complex in Arabidopsis (EAF1 and EPL1) and show their roles in photosynthesis genes regulation through H4K5ac and H2A.Z acetylation.
- Tomasz Bieluszewski
- , Weronika Sura
- & Piotr A. Ziolkowski
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Article
| Open AccessA plant virus satellite RNA directly accelerates wing formation in its insect vector for spread
The cucumber mosaic virus is accompanied by short RNA molecules, satellite RNAs. This study shows that leaves infected with Y-satellite RNA preferentially attract aphids and manipulate aphid physiology to promote their spread to neighbouring plants.
- Wikum H. Jayasinghe
- , Hangil Kim
- & Chikara Masuta
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Article
| Open AccessHeterochromatin is a quantitative trait associated with spontaneous epiallele formation
The molecular origins of epialleles remain unknown. Here, the authors show that a positive feedback loop between H3K9me2 and CMT2/3 is a major contributing factor to the origins of spontaneous epialleles and that heterochromatin is a quantitative trait associated with spontaneous epiallele formation.
- Yinwen Zhang
- , Hosung Jang
- & Robert J. Schmitz
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Article
| Open AccessInitiation of cytosolic plant purine nucleotide catabolism involves a monospecific xanthosine monophosphate phosphatase
Dephosphorylation of xanthosine monophosphate (XMP) initiates purine nucleotide catabolism in plant cells. Here the authors identify an XMP phosphatase from Arabidopsis that channels XMP towards catabolism in vivo and demonstrate the structural basis for its XMP specificity.
- Katharina J. Heinemann
- , Sun-Young Yang
- & Claus-Peter Witte
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Article
| Open AccessThe parent-of-origin lncRNA MISSEN regulates rice endosperm development
The cereal endosperm is a major determinant of seed size and shape. Here the authors show that a lncRNA, MISSEN, is expressed from the maternally derived allele in rice seeds and regulates a helicase family protein to support efficient nuclear division, distribution and cellularization in the endosperm.
- Yan-Fei Zhou
- , Yu-Chan Zhang
- & Yue-Qin Chen
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Article
| Open AccessDirect photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B
Photoactivated phytochrome B regulates gene expression by interacting with PIF transcription factors. Here the authors show that PIF3 contains a p53-like transcription activation domain (AD) and that PHYB can directly suppress PIF3 transactivation activity by binding adjacent to the AD.
- Chan Yul Yoo
- , Jiangman He
- & Meng Chen
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Article
| Open AccessThe intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors
MADS transcription factors regulate multiple aspects of plant development. Here the authors show that the intervening I domain is conserved in both type I and type II plant MADS lineages and contributes to the functional identity of the protein by influencing both DNA binding activity and dimerisation specificity.
- Xuelei Lai
- , Rosario Vega-Léon
- & Chloe Zubieta
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Article
| Open AccessArabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation
MORC ATPases are required for transposable element silencing and heterochromatin condensation in plants and animals. Here the authors show that Arabidopsis MORCs colocalize with sites of RNA-directed DNA methylation and provide evidence that they act as molecular tethers to efficiently establish DNA methylation.
- Yan Xue
- , Zhenhui Zhong
- & Steven E. Jacobsen
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Article
| Open AccessIdentification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton
Blue light penetrates deeper than red light in ocean, thus blue light sensing is critical for adaptation to marine environments. Here, the authors report the genome of Pyconococcus provasolii and identify a chimeric dual orange/far-red and blue light receptor composed of a phytochrome and a cryptochrome by analyzing the marine metagenomes.
- Yuko Makita
- , Shigekatsu Suzuki
- & Minami Matsui
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Article
| Open AccessH3K27me3 demethylases alter HSP22 and HSP17.6C expression in response to recurring heat in Arabidopsis
Acclimation to high temperature increases tolerance of heat shock in plants. Here the authors show that JUMONJI H3K27me3 demethylases are needed for heat acclimation in Arabidopsis and act at loci encoding HEAT SHOCK PROTEINS to facilitate induction upon heat stress.
- Nobutoshi Yamaguchi
- , Satoshi Matsubara
- & Toshiro Ito
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Article
| Open AccessHeteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis
Moderate heat stress primes plants to acquire tolerance to subsequent, more severe heat stress. Here the authors show that the HSFA3 transcription factor forms a heteromeric complex with HSFA2 to sustain activated transcription of genes required for acquired thermotolerance by promoting H3K4 hyper-methylation.
- Thomas Friedrich
- , Vicky Oberkofler
- & Isabel Bäurle
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Article
| Open AccessA recombined Sr26 and Sr61 disease resistance gene stack in wheat encodes unrelated NLR genes
The tall wheat grass-derived stem rust resistance genes Sr26 and Sr61 are among a few ones that are effective to all current dominant races of stem rust, including Ug99. Here, the authors show that the two genes are present in a small non-recombinogenic segment but encode two unrelated NLR proteins.
- Jianping Zhang
- , Timothy C. Hewitt
- & Evans S. Lagudah
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Article
| Open AccessGenome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics
Advances in omics provide a tool to understand mechanisms for plant–microbial interactions under stress. Here the authors apply genome-resolved metagenomics to investigate sorghum and its microbiome responses to drought, identifying an unexpected role of iron metabolism.
- Ling Xu
- , Zhaobin Dong
- & Devin Coleman-Derr
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Article
| Open AccessEctopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase
The ability to target DNA methylation to specific loci is important for both basic and applied research. Here, the authors fuse CG-specific methyltransferase SssI with an artificial zinc finger protein for DNA methylation targeting and show the chromatin features favorable for efficient gain of methylation.
- Wanlu Liu
- , Javier Gallego-Bartolomé
- & Steven E. Jacobsen
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Article
| Open AccessSingle-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root
Root meristems give rise to distinct cell types that differentiate across defined temporal and spatial gradients. Here, via single-cell RNA sequencing and surveying chromatin accessibility the authors profile gene expression of different cell types during rice root development.
- Tian-Qi Zhang
- , Yu Chen
- & Jia-Wei Wang