Identification of miRNA858 long-loop precursors in seed plants.

MicroRNAs (miRNAs) are a class of nonprotein-coding short transcripts that provide a layer of post-transcriptional regulation essential to many plant biological processes. MiR858, which targets the transcripts of MYB transcription factors, can affect a range of secondary metabolic processes. Although miR858 and its 187-nt precursor have been well studied in Arabidopsis (Arabidopsis thaliana), a systematic investigation of miR858 precursors and their functions across plant species is lacking due to a problem in identifying the transcripts that generate this subclass. By re-evaluating the transcript of miR858 and relaxing the length cut-off for identifying hairpins, we found in kiwifruit (Actinidia chinensis) that miR858 has long-loop hairpins (1,100 to 2,100 nt), whose intervening sequences between miRNA generating complementary sites were longer than all previously reported miRNA hairpins. Importantly, these precursors of miR858 containing long-loop hairpins (termed MIR858L) are widespread in seed plants including Arabidopsis, varying between 350 and 5,500 nt. Moreover, we showed that MIR858L has a greater impact on proanthocyanidin and flavonol levels in both Arabidopsis and kiwifruit. We suggest that an active MIR858L-MYB regulatory module appeared in the transition of early land plants to large upright flowering plants, making a key contribution to plant secondary metabolism.

Intrinsically disordered proteins SAID1/2 condensate on SERRATE for dual inhibition of miRNA biogenesis in Arabidopsis.

Intrinsically disordered proteins (IDPs) SAID1/2 are hypothetic dentin sialophosphoprotein-like proteins, but their true functions are unknown. Here, we identified SAID1/2 as negative regulators of SERRATE (SE), a core factor in miRNA biogenesis complex (microprocessor). Loss-of-function double mutants of said1; said2 caused pleiotropic developmental defects and thousands of differentially expressed genes that partially overlapped with those in se. said1; said2 also displayed increased assembly of microprocessor and elevated accumulation of microRNAs (miRNAs). Mechanistically, SAID1/2 promote pre-mRNA processing 4 kinase A-mediated phosphorylation of SE, causing its degradation in vivo. Unexpectedly, SAID1/2 have strong binding affinity to hairpin-structured pri-miRNAs and can sequester them from SE. Moreover, SAID1/2 directly inhibit pri-miRNA processing by microprocessor in vitro. Whereas SAID1/2 did not impact SE subcellular compartmentation, the proteins themselves exhibited liquid-liquid phase condensation that is nucleated on SE. Thus, we propose that SAID1/2 reduce miRNA production through hijacking pri-miRNAs to prevent microprocessor activity while promoting SE phosphorylation and its destabilization in Arabidopsis.

The effect of weak π-π interactions on single-molecule electron transport properties of the tetraphenylethene molecule and its derivatives: a first-principles study.

Intramolecular π-π interactions are a significant research focus in fields such as chemistry, biology, and materials science. Different configurations of benzene-benzene moieties within a molecule can affect the magnitude of their π-π interactions, consequently influencing the electronic transport capabilities of the molecule. In this study, we designed three π-conjugated molecules, TPEM, TPEEM, and TEEPM, based on tetraphenylethene (TPE). These three molecules exhibit three distinct π-conjugated structures: linear cis-π-conjugation, linear trans-π-conjugation, and cross-π-conjugation. Thereinto, TPEM and TPEEM molecules share the same TPE core, with identical π-π interaction distances, while the TEEPM molecule has acetylene groups between the TPE units, thereby increasing the π-π interaction distances between the benzene moieties. Using density functional theory calculations combined with non-equilibrium Green's function (DFT+NEGF), our results reveal that the conductance order of different π-conjugated structures in TPEM and TPEEM molecules is as follows: cis > cross ≈ trans. Through analysis of transmission spectra, transmission pathways, and the innermost π orbitals, we find that in TPEM and TPEEM molecules, the cis- and cross-π-conjugated structures exhibit π-π interactions between benzene moieties and provide special through-space electron transport pathways, enhancing their electronic transport capabilities in coordination with the bonded molecular framework, whereas their trans-conjugated structures only allow electron transport along the molecular backbone. In contrast, in TEEPM molecule, due to the absence of π-π interactions, the conductance of different π-conjugated structures is primarily determined by the molecular backbone and follows the order: trans > cis > cross. These findings provide a theoretical basis for designing single-molecule electronic devices with multiple electron channels based on intramolecular π-π interactions.

SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via Serrate to impede miRNA production.

Chromatin remodelling factors (CHRs) typically function to alter chromatin structure. CHRs also reside in ribonucleoprotein complexes, but little is known about their RNA-related functions. Here we show that CHR2 (also known as BRM), the ATPase subunit of the large switch/sucrose non-fermentable (SWI/SNF) complex, is a partner of the Microprocessor component Serrate (SE). CHR2 promotes the transcription of primary microRNA precursors (pri-miRNAs) while repressing miRNA accumulation in vivo. Direct interaction with SE is required for post-transcriptional inhibition of miRNA accumulation by CHR2 but not for its transcriptional activity. CHR2 can directly bind to and unwind pri-miRNAs and inhibit their processing, and this inhibition requires the remodelling and helicase activity of CHR2 in vitro and in vivo. Furthermore, the secondary structures of pri-miRNAs differed between wild-type Arabidopsis thaliana and chr2 mutants. We conclude that CHR2 accesses pri-miRNAs through SE and remodels their secondary structures, preventing downstream processing by DCL1 and HYL1. Our study uncovers pri-miRNAs as a substrate of CHR2, and an additional regulatory layer upstream of Microprocessor activity to control miRNA accumulation.

A new and effective two-step clustering approach for single cell RNA sequencing data.

BACKGROUND: The rapid devolvement of single cell RNA sequencing (scRNA-seq) technology leads to huge amounts of scRNA-seq data, which greatly advance the research of many biomedical fields involving tissue heterogeneity, pathogenesis of disease and drug resistance etc. One major task in scRNA-seq data analysis is to cluster cells in terms of their expression characteristics. Up to now, a number of methods have been proposed to infer cell clusters, yet there is still much space to improve their performance. RESULTS: In this paper, we develop a new two-step clustering approach to effectively cluster scRNA-seq data, which is called TSC - the abbreviation of Two-Step Clustering. Particularly, by dividing all cells into two types: core cells (those possibly lying around the centers of clusters) and non-core cells (those locating in the boundary areas of clusters), we first clusters the core cells by hierarchical clustering (the first step) and then assigns the non-core cells to the corresponding nearest clusters (the second step). Extensive experiments on 12 real scRNA-seq datasets show that TSC outperforms the state of the art methods. CONCLUSION: TSC is an effective clustering method due to its two-steps clustering strategy, and it is a useful tool for scRNA-seq data analysis.

A competition-attenuation mechanism modulates thermoresponsive growth at warm temperatures in plants.

Global warming has profound impact on growth and development, and plants constantly adjust their internal circadian clock to cope with external environment. However, how clock-associated genes fine-tune thermoresponsive growth in plants is little understood. We found that loss-of-function mutation of REVEILLE5 (RVE5) reduces the expression of circadian gene EARLY FLOWERING 4 (ELF4) in Arabidopsis, and confers accelerated hypocotyl growth under warm-temperature conditions. Both RVE5 and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) accumulate at warm temperatures and bind to the same EE cis-element presented on ELF4 promoter, but the transcriptional repression activity of RVE5 is weaker than that of CCA1. The binding of CCA1 to ELF4 promoter is enhanced in the rve5-2 mutant at warm temperatures, and overexpression of ELF4 in the rve5-2 mutant background suppresses the rve5-2 mutant phenotype at warm temperatures. Therefore, the transcriptional repressor RVE5 finetunes ELF4 expression via competing at a cis-element with the stronger transcriptional repressor CCA1 at warm temperatures. Such a competition-attenuation mechanism provides a balancing system for modulating the level of ELF4 and thermoresponsive hypocotyl growth under warm-temperature conditions.

Rice chromatin protein OsHMGB1 is involved in phosphate homeostasis and plant growth by affecting chromatin accessibility.

Although phosphorus is one of the most important essential elements for plant growth and development, the epigenetic regulation of inorganic phosphate (Pi) signaling is poorly understood. In this study, we investigated the biological function and mode of action of the high-mobility-group box 1 protein OsHMGB1 in rice (Oryza sativa), using molecular and genetic approaches. We determined that OsHMGB1 expression is induced by Pi starvation and encodes a nucleus-localized protein. Phenotypic analysis of Oshmgb1 mutant and OsHMGB1 overexpression transgenic plants showed that OsHMGB1 positively regulates Pi homeostasis and plant growth. Transcriptome deep sequencing and chromatin immunoprecipitation followed by sequencing indicated that OsHMGB1 regulates the expression of a series of phosphate starvation-responsive (PSR) genes by binding to their promoters. Furthermore, an assay for transposase-accessible chromatin followed by sequencing revealed that OsHMGB1 is involved in maintaining chromatin accessibility. Indeed, OsHMGB1 occupancy positively correlated with genome-wide chromatin accessibility and gene expression levels. Our results demonstrate that OsHMGB1 is a transcriptional facilitator that regulates the expression of a set of PSR genes to maintain Pi homeostasis in rice by increasing the chromatin accessibility, revealing a key epigenetic mechanism that fine-tune plant acclimation responses to Pi-limited environments.

Molecular mechanisms and genetic improvement of low-phosphorus tolerance in rice.

Phosphorus (P) is a macronutrient required for plant growth and reproduction. Orthophosphate (Pi), the preferred P form for plant uptake, is easily fixed in the soil, making it unavailable to plants. Limited phosphate rock resources, low phosphate fertilizer use efficiency and high demands for green agriculture production make it important to clarify the molecular mechanisms underlying plant responses to P deficiency and to improve plant phosphate efficiency in crops. Over the past 20 years, tremendous progress has been made in understanding the regulatory mechanisms of the plant P starvation response. Here, we systematically review current research on the mechanisms of Pi acquisition, transport and distribution from the rhizosphere to the shoot; Pi redistribution and reuse during reproductive growth; and the molecular mechanisms of arbuscular mycorrhizal symbiosis in rice (Oryza sativa L.) under Pi deficiency. Furthermore, we discuss several strategies for boosting P utilization efficiency and yield in rice.

Why Ligand Doping Increases the Fluorescence of an Anthracene-Based Metal-Organic Framework.

Metal-organic frameworks (MOFs) built from fluorescent ligands frequently exhibit enhanced fluorescence when doped with inert ligands. This study focuses on a MOF of the UiO-68 structure, which is built from a fluorescent dibenzoate-anthracene ligand doped with a dibenzoate-benzene ligand. Our investigation aims to understand the mechanism behind the doping-enhanced emission of this MOF. We rule out several possible mechanisms, including exciton coupling, electron transfer between ligand and metal center, and ligand intersystem crossing induced by the metal center. Inhibition of the interligand charge transfer is considered a possible way to enhance emission. Furthermore, we propose that the conformational change of the anthracene-based ligand in the MOF cavity is also a way for enhancement. Our molecular dynamics simulations of the MOF structure filled with solvents reveal that the steric crowding in the cavity induces a conformational change at different doping levels, affecting the rate of intersystem crossing of the ligand.

Recovery and utilization of waste filtrate from industrial biological fermentation: Development and metabolite profile of the Bacillus cereus liquid bio-fertilizer.

Most fermentation waste filtrates can be used as raw materials for producing bio-fertilizers to reduce wastewater emissions and environmental pollution, but their bio-fertilizer utilization depends on the nutrients contained and their metabolized by functional microorganism. To achieve bio-fertilizer utilization of Acremonium terricola fermented waste filtrate, this study systematically explored the functional microbial species for making good use of waste liquid, optimized material process parameters for bio-fertilizer production based on D-optimal mixture design method, and analyzed the composition of the waste filtrate and its metabolism by functional microorganisms using a non-targeted LC-MS metagenomics technique. The results showed that Bacillus cereus was the functional microbial candidate for producing bio-fertilizer because of its more efficiently utilize the waste filtrate than other Bacillus sp. The optimal material process parameters of the liquid bio-fertilizer were the inoculum dose of 5% (v:v, %), 80% of waste filtrate, 0.25% of N, 3.5% of P2O5, 3.25% of K2O of mass percentage. Under these conditions, the colony forming unit (CFU) of Bacillus cereus could reach (1.59 ± 0.01) × 108 CFU/mL, which met the bio-fertilizer standard requirements of the People's Republic of China (NY/T798). Furthermore, the potential functions of bio-fertilizer were studied based on comparison of raw materials and production components: on the one hand, waste filtrate contained abundant of nitrogen and carbon sources, and bioactive substances secreted by Acremonium terricola, such as ß-alanyl-L-lysine, anserine, UMP, L-lactic acid and etc., which could meet the nutrient requirements of the growth of Bacillus cereus; On the other hand, some compounds of waste filtrate with the potential to benefit the plant growth and defense, such as betaine aldehyde, (2E,6E)-farnesol, homogentisic acid and etc., were significantly up regulated by Bacillus cereus utilization of the filtrate. To sum up, this work highlighted that the waste filtrate could be efficiently developed into liquid bio-fertilizer by Bacillus cereus.

Root-secreted peptide OsPEP1 regulates primary root elongation in rice.

Hormone-like signaling peptides play essential roles in plant growth and development; however, few peptides regulating root development have been identified in rice (Oryza sativa). Here, we combined liquid chromatography-tandem mass spectrometry (LC-MS/MS) with whole-genome in silico screening for root-secreted peptides in rice. We identified the five-amino-acid PEPTIDE 1 (PEP1) encoded by OsPEP1 (LOC_Os11g09560). OsPEP1 was expressed highly in root tissues, especially root cap cells and epidermal cells in the root maturation zone. Exogenous application of PEP1 inhibited primary root growth. Notably, OsPEP1 RNA interference (RNAi) lines had short primary roots with small meristems and short cells in the root elongation zone; furthermore, the short root phenotype of OsPEP1 RNAi plants could be rescued by exogenous application of PEP1. Our transcriptome data further revealed that PEP1 could reprogram the expression of genes in different pathways, including oxidation-reduction. OsPEP1 overexpression lines similarly displayed short roots, although this phenotype was not rescued by exogenous PEP1. These results suggest that root growth can be inhibited by both too much and too little PEP1. Our findings highlight PEP1 as a candidate plant peptide hormone regulating root development in rice.

Complete Genome Sequence of Pythium oligandrum, Isolated from Rhizosphere Soils of Chinese Angelica sinensis.

Most of the Pythium species are pathogenic to a wide range of economically important crops and, sometimes, can even cause diseases in animals and humans. An exception is that the soil-inhabiting P. oligandrum is an effective biocontrol agent against a diverse suite of pathogens and promotes plant growth. In this work, we sequenced the whole genome of P. oligandrum PO-1, isolated from rhizosphere soils of Chinese Angelica sinensis, using a combination of long-read single-molecule real-time sequencing technology (Pacific Biosciences [PacBio]) and Illumina sequencing. The 2.5-Gb and 5.2-Gb bases were generated respectively. The sequencing depths were 93× with PacBio and 145× with Illumina sequencing. With the PacBio sequencing results further corrected by Illumina sequencing, the genome was assembled into 71 scaffolds with a total size of 39.10 Mb (N50 = 1.45 Mb; L50 = 9)and the longest scaffold is 3.49 Mb. Genome annotation identifies 15,632 protein-coding genes and 0.47 Mb of transposable elements. Our genomic assembly and annotation have been greatly improved compared with the already released three genomes of P. oligandrum. This genomic data will provide valuable information to understand the mechanism underlying its biocontrol potentials and will also facilitate the dissection of genome evolution and environmental adaptation within the genus Pythium. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.

Two-Photon 3D Printing in Metal-Organic Framework Single Crystals.

Two-photon polymerization (TPP) is a micro/nano-fabrication technology for additive manufacturing, enabling 3D printing of polymeric materials using ultrafast laser pulses. In this work, two-photon polymerization is realized inside a metal-organic framework (MOF) crystal. Intricate structures are built in the porous crystal to create a microstructure-in-crystal hybrid. Furthermore, the MOF can be removed by acid treatment to release the printed structure. The two-photon polymerization inside the crystal has the potential for MOF sensing device fabrication and data storage applications. In the future development, printing different materials in the same MOF crystal for creating functional 3D devices is hoped.

Mechanistic Investigation and Conductance Modulation of a Metal-Molecule-Metal Junction via Extra Acid Addition.

One important prerequisite for the fabrication of molecular functional device strongly relies on the understanding the conducting behaviors of the metal-molecule-metal junction that can respond to an external stimulus. The model Lewis basic molecule 4,4'-(pyridine-3,5-diyl)dibenzonitrile (DBP), which can react with Lewis acid and protic acid, was synthesized. Then, the molecular conducting behavior of DBP, DBP-B(C6 F5 )3 , and DBP-TfOH (DBP-B(C6 F5 )3 , and DBP-TfOH were produced by Lewis acid and protonic acid treatment of DBP) was researched and compared. Given that their identical physical paths for DBP, DBP-B(C6 F5 )3 , and DBP-TfOH to sustain charge transport, our results indicate that modifying the molecular electronic structure, even not directly changing the conductive physical backbone, can tune the charge transporting ability by nearly one order of magnitude. Furthermore, the addition of another Lewis base triethylamine (of stronger alkaline than DBP), to Lewis acid-base pair reverts the electrical properties back to that of a single DBP junction, that is constructive to propose a useful but simple strategy for the design and construction of reversible and controllable molecular device based on pyridine derived molecule.

Pseudomonas tumuqii sp. nov., isolated from greenhouse soil.

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, named LAMW06T, was isolated from greenhouse soil in Beijing, China. In the 16S rRNA gene sequence comparison, strain LAMW06T had the highest similarity with Pseudomonas cuatrocienegasensis 1NT. Phylogenetic analysis based on the 16S rRNA and three housekeeping gene sequences (gyrB, rpoB and rpoD) indicated that strain represented a member of the genus Pseudomonas. The genome sequence size of the isolate was 5.5 Mb, with a DNA G + C content of 63.5 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain LAMW06T and closely related members of Pseudomonas borbori R-20821T, Pseudomonas taeanensis MS-3T and P. cuatrocienegasensis 1NT were 90.9%, 82.4%, 81.5% and 43.0%, 25.9%, 24.6% respectively. The major fatty acids contained summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C18:1 ω7c and C16:0. The primary respiratory quinone was ubiquinone-9. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, six aminophospholipids, six phospholipids, one aminolipid and one glycolipid. According to the genotypic, phylogenetic and chemotaxonomic data, strain LAMW06T represents a novel species within the genus Pseudomonas, for which the name Pseudomonas tumuqii sp. nov. is proposed. The type strain is LAMW06T (= GDMCC 1.2003T = KCTC 72829T).

Chryseobacterium subflavum sp. nov., isolated from soil.

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated LAMRS1T, was isolated from a soil sample collected in Hebei Province, PR China. Strain LAMRS1T was able to grow optimally in the presence of 0.5 % (w/v) NaCl, at pH 7.5 and at 30 °C. On the basis of 16S rRNA gene sequence analysis, strain LAMRS1T was closely related to members of the genus Chryseobacterium, with highest levels of sequence similarity to Chryseobacterium soli DSM 19298T (97.9 %), Chryseobacterium soldanellicola DSM 17072T (97.6%) and Chryseobacterium piperi CTMT (97.5 %). The average nucleotide identity and digital DNA-DNA hybridization values between LAMRS1T and the closely related species of C. soli DSM 19298T, C. soldanellicola DSM 17072T and C. piperi CTMT were 78.1, 78.2 and 80.7 %, and 21.7, 22.0 and 23.7 %, respectively. The draft genome sequence of LAMRS1T was 4.61 Mb, with DNA G+C content of 36.2 mol%. The major isoprenoid quinone was menaquinone-6 and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) constituted the major cellular fatty acids. The main polar lipids were phosphatidylethanolamine, four aminolipids, three glycolipids and seven unidentified lipids. On the basis of evidence presented in this study, strain LAMRS1T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium subflavum sp. nov. is proposed. The type strain is LAMRS1T (=JCM 33868T=KCTC 72823T).

Dynamic Interconversions of Single Molecules Probed by Recognition Tunneling at Cucurbit[7]uril-Functionalized Supramolecular Junctions.

We introduce a versatile recognition tunneling technique using doubly cucurbit[7]uril-functionalized electrodes to form supramolecular junctions that capture analytes dynamically by host-guest complexation. This results in characteristic changes in their single-molecule conductance. For structurally related drug molecules (camptothecin, sanguinarine, chelerythrine, and berberine) and mixtures thereof, we observed distinct current switching signals related to their intrinsic conductance properties as well as pH-dependent effects which can be traced back to their different states (protonated versus neutral). The conductance variation of a single molecule with pH shows a sigmoidal distribution, allowing us to extract a pKa value for reversible protonation, which is consistent with the reported macroscopic results. The new electronic method allows the characterization of unmodified drug molecules and showcases the transfer of dynamic supramolecular chemistry principles to single molecules.

Photoactivation of Cu Centers in Metal-Organic Frameworks for Selective CO2 Conversion to Ethanol.

CO2 hydrogenation to ethanol is of practical importance but poses a significant challenge due to the need of forming one C-C bond while keeping one C-O bond intact. CuI centers could selectively catalyze CO2-to-ethanol conversion, but the CuI catalytic sites were unstable under reaction conditions. Here we report the use of low-intensity light to generate CuI species in the cavities of a metal-organic framework (MOF) for catalytic CO2 hydrogenation to ethanol. X-ray photoelectron and transient absorption spectroscopies indicate the generation of CuI species via single-electron transfer from photoexcited [Ru(bpy)3]2+-based ligands on the MOF to CuII centers in the cavities and from Cu0 centers to the photoexcited [Ru(bpy)3]2+-based ligands. Upon light activation, this Cu-Ru-MOF hybrid selectively hydrogenates CO2 to EtOH with an activity of 9650 µmol gCu-1 h-1 under 2 MPa of H2/CO2 = 3:1 at 150 °C. Low-intensity light thus generates and stabilizes CuI species for sustained EtOH production.

Nanoscale Metal-Organic Frameworks and Metal-Organic Layers with Two-Photon-Excited Fluorescence.

Metal-organic frameworks (MOFs) based on 9,10-diphenylanthracene-derived ligands had been reported to exhibit upconverted fluorescence through triplet-triplet annihilation. We found that zirconium MOFs based on 9,10-diphenylanthracene can also give upconverted fluorescence via two-photon absorption without adding a triplet photosensitizer when a femtosecond pulsed laser is used as the excitation source. By tuning the synthetic condition, we obtained nanoscale MOFs of UiO structure in both octahedral and hexagonal nanoplate shapes, as well as a hexagonal nanoplate of MOFs of hcp-UiO structure and two-dimensional metal-organic layers. All of them, as well as a homogeneous solution of the 9,10-diphenylanthracene ligand, exhibit upconverted fluorescence upon excitation using a laser pulse of 60 fs with a pulse energy of ∼1.1 × 106 nJ/cm2 (unfocused). Moreover, we observed different emission spectra by two-photon excitation compared to those by one-photon excitation, which indicates access to a unique initial excited state via two-photon excitation. This phenomenon is not observed for a homogeneous solution of the ligand. These nanoscale MOFs may find application in two-photon fluorescence imaging.

Genome-wide probing RNA structure with the modified DMS-MaPseq in Arabidopsis.

Transcripts have intrinsic propensity to form stable secondary structure that is fundamental to regulate RNA transcription, splicing, translation, RNA localization and turnover. Numerous methods that integrate chemical reactions with next-generation sequencing (NGS) have been applied to study in vivo RNA structure, providing new insights into RNA biology. Dimethyl sulfate (DMS) probing coupled with mutational profiling through NGS (DMS-MaPseq) is a newly developed method for revealing genome-wide or target-specific RNA structure. Herein, we present our experimental protocol of a modified DMS-MaPseq method for plant materials. The DMS treatment condition was optimized, and library preparation procedures were simplified. We also provided custom scripts for bioinformatic analysis of genome-wide DMS-MaPseq data. Bioinformatic results showed that our method could generate high-quality and reproducible data. Further, we assessed sequencing depth and coverage for genome-wide RNA structure profiling in Arabidopsis, and provided two examples of in vivo structure of mobile RNAs. We hope that our modified DMS-MaPseq method will serve as a powerful tool for analyzing in vivo RNA structurome in plants.