Jixian Zhai

• Ph.D + MS**3
• Professor (Associate) at Southern University of Science and Technology

RNA-directed DNA methylation in Arabidopsis thaliana is driven by the plant-specific RNA Polymerase IV (Pol IV). It has been assumed that a Pol IV transcript can give rise to multiple 24-nt small interfering RNAs (siRNAs) that target DNA methylation. Here, we demonstrate that Pol IV-dependent RNAs (P4RNAs) from wild-type Arabidopsis are surprisingl...

Significance By RNA profiling of 10 stages of maize anthers plus mature pollen, we found two distinct classes of phased small-interfering RNAs (phasiRNAs): 21-nt premeiotic phasiRNAs, after germinal and somatic cell specification, and 24-nt meiotic phasiRNAs coordinately accumulated during meiosis and persist into pollen. Sequencing of RNA from fiv...

Plant small RNAs are 3' methylated by the methyltransferase HUA1 ENHANCER1 (HEN1). In plant hen1 mutants, 3' modifications of small RNAs, including oligo-uridylation (tailing), are associated with accelerated degradation of microRNAs (miRNAs). By sequencing small RNAs of the wild type and hen1 mutants from Arabidopsis thaliana, rice (Oryza sativa),...

Legumes and many nonleguminous plants enter symbiotic interactions with microbes, and it is poorly understood how host plants respond to promote beneficial, symbiotic microbial interactions while suppressing those that are deleterious or pathogenic. Trans-acting siRNAs (tasiRNAs) negatively regulate target transcripts and are characterized by siRNA...

Progress in epigenetics has revealed mechanisms that can heritably regulate gene function independent of genetic alterations. Nevertheless, little is known about the role of epigenetics in evolution. This is due in part to scant data on epigenetic variation among natural populations. In plants, small interfering RNA (siRNA) is involved in both the...

Light plays a central role in plant growth and development, providing an energy source and governing various aspects of plant morphology. Previous study showed that many polyadenylated full-length RNA molecules within the nucleus contain unspliced introns (post-transcriptionally spliced introns, PTS introns), which may play a role in rapidly respon...

Establishing legume–rhizobial symbiosis requires precise coordination of complex responses in a time- and cell type-specific manner. Encountering Rhizobium, rapid changes of gene expression levels in host plants occur in the first few hours, which prepare the plants to turn off defence and form a symbiotic relationship with the microbes. Here, we a...

Cytonuclear disruption may accompany allopolyploid evolution as a consequence of the merger of different nuclear genomes in a cellular environment having only one set of progenitor organellar genomes. One path to reconcile potential cytonuclear mismatch is biased expression for maternal gene duplicates (homoeologs) encoding proteins that target to...

The short read-length of next-generation sequencing makes it challenging to characterize highly repetitive regions (HRRs) such as centromeres, telomeres and ribosomal DNAs. Based on recent strategies that combined long-read sequencing and exogenous enzymatic labelling of open chromatin, we developed single-molecule targeted accessibility and methyl...

Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell atlas of soybean nodules and roots. In central infected zones of nodules, we found that uninfected cells specialize into functionally distinct subgroups during nodule developme...

Intron retention is the most common alternative splicing event in plants and plays a crucial role in the responses of plants to environmental signals. Despite a large number of RNA-seq libraries from different treatments and genetic mutants stored in public domains, a resource for querying the intron-splicing ratio of individual intron is still req...

Poly(A) tail is a hallmark of eukaryotic messenger RNA and its length plays an essential role in regulating mRNA metabolism. However, a comprehensive resource for plant poly(A) tail length has yet to be established. Here, we applied a poly(A)-enrichment-free, nanopore-based method to profile full-length RNA with poly(A) tail information in plants....

In Arabidopsis, DICER-LIKE PROTEIN 3 (DCL3) cuts the substrate pre-siRNA into a product siRNA duplex, encompassing one 23-nt strand and one 24-nt strand. To monitor the separation of the siRNA duplex with only 1-nt difference, we developed this protocol to evaluate the in vitro dicing activity of DCL3. The method can be applied for measuring the le...

Ready to dice In the biogenesis of small RNAs, the Dicer family endonucleases act as a molecular ruler to cut the substrate RNA into defined lengths. Wang et al . report a structure of the dicing-competent state of plant DICER LIKE PROTEIN 3 (DCL3) in complex with a pre–small interfering RNA (pre-siRNA). Toward one end of the pre-siRNA, DCL3 uses a...

[This corrects the article DOI: 10.1371/journal.pbio.2001272.].

Mediator 12 (MED12) and MED13 are components of the Mediator multi-protein complex, that facilitates the initial steps of gene transcription. Here, in an Arabidopsis mutant screen, we identify MED12 and MED13 as positive gene regulators, both of which contribute broadly to morc1 de-repressed gene expression. Both MED12 and MED13 are preferentially...

Small RNAs regulate chromatin modifications such as DNA methylation and gene silencing across eukaryotic genomes. In plants, RNA-directed DNA methylation (RdDM) requires 24-nucleotide small interfering RNAs (siRNAs) that bind to ARGONAUTE 4 (AGO4) and target genomic regions for silencing. RdDM also requires non-coding RNAs transcribed by RNA polyme...

Supplementary Figure 1. Modified GRO-seq is able to capture nascent Pol V-dependent transcripts. a, Scatterplot of signals from two independent GRO-seq experiments in Col-0. The Pearson’s correlation coefficient is calculated and shown on the plot. b, Metaplot showing GRO-seq signals over Pol V-occupied regions in Col-0 and nrpe1. c, Metaplot showi...

Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the landscape of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis, and a tremendous amount of WGBS data has been generated by the research community. However, th...

Heavy metals (HMs) contamination on agricultural lands not only reduces crop yield but also causes human health concerns. As a plant gasotransmitter, hydrogen sulfide (H2 S) can trigger various defense responses and help reduce HMs accumulation in plants; however, little is known about the regulatory mechanisms of H2 S signaling. Here, we provided...

The degradation of small RNAs in plants and animals is associated with small RNA 3′ truncation and 3′ uridylation and thus relies on exonucleases and nucleotidyl transferases. ARGONAUTE (AGO) proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. AGO1 is the microRNA (miRNA) ef...

Matrices representing the compositions of reads for various miRNAs in hen1 and hen1 sdn1 sdn2 libraries. The X axis represents the number of nucleotides truncated from the 3′ end. The Y axis represents the number of nucleotides added to the 3′ end. The relative proportions of the species are indicated by the sizes of the circles. Two biological rep...

Hierarchical clustering analysis showing the degree of similarity among the sRNA-seq libraries. Sample-to-sample distances were calculated based on log-transformed normalized read counts. The biological replicates of each sample type were highly reproducible. The raw data can be found in S1 Data file. (TIF)

Composition of miRNAs in Col, sdn1 sdn2, hen1, and hen1 sdn1 sdn2. (XLSX)

Composition of miRNA forms in AGO10 OE and sdn1 sdn2 AGO10 OE. (XLSX)

Oligonucleotides used in this study. (DOCX)

A model of miRNA degradation. SDNs initiate degradation by trimming the miRNA to result in a 3′ truncated and unmethylated miRNA, which is uridylated by HESO1 or URT1. The tailed species are further degraded by an as yet unknown enzyme. SDN1 (this study) and the nucleotidyl transferases (HESO1 and URT1) can act on AGO1-bound miRNAs as well as free...

Matrices representing the compositions of miR165/6 reads in AGO10 OE and sdn1 sdn2 AGO10 OE libraries. Total small RNAs were sequenced from seedling tissues (“s”) of one pair (I) of transgenic lines (AGO10 OE and sdn1 sdn2 AGO10 OE) and inflorescence tissues (“f”) of another independent pair (II) of transgenic lines. AGO10 over expression in the sd...

Composition of miRNA forms in Col, AGO10 OE S1, and AGO10 OE 4mAGO1. (XLSX)

Profile of AGO1- and AGO10-bound miRNAs in AGO10 OE S1. (XLSX)

Composition of miRNA forms in AGO1 IP from various AGO10 OE lines (S2, M1, M2, and W1). (XLSX)

SDN1 enzymatic assays with AGO1 and AGO10 immunoprecipitates as substrates. Immunoprecipitation (IP) was performed with wild type (Col) or a line with the His-Flag-AGO10 transgene in an ago10 mutant background [5]. AGO1 and AGO10 IP was performed with anti-AGO1 and anti-Flag antibodies, respectively. (A) The AGO1 IP was subjected to western blottin...

Characterization of AGO10 over expression lines. (A) Real-time RT-PCR to quantify transcript levels of AGO1 and AGO10 in wild type (Col) and AGO10 OE S1. ** p-value < 0.01, *** p-value < 0.001. (B) Real-time RT-PCR to detect pri/pre-miR165/6 from eight MIR165/6 genes that were expressed in seedlings. (C) Northern blotting to detect pre-miR166a in t...

Matrices representing the compositions of miR165/6 reads in Col, AGO10 OE S1 and AGO10 OE 4mAGO1 libraries. miR165/6 3′ truncation was increased in AGO10 OE S1 relative to wild type. 4mAGO1 failed to rescue this increase in miR165/6 3′ truncation. The data were based on one biological replicate. Underlying data can be found in the GEO database as s...

Raw data for all figures and supplemental figures. (XLSX)

Composition of miRNAs in hen1 and hen1 heso1. (XLSX)

Composition of miRNA forms in AGO1 IP and AGO10 IP treated with mock (no enzyme), SDN1, and SDN1 catalytic mutant (SDN1D283A). (XLSX)

Composition of miRNA forms in Col and various AGO10 OE lines (S2, M1, M2, and W1). (XLSX)

Composition of miRNA forms in Col and AGO10 OE S1. (XLSX)

Profile of AGO1-bound miRNAs in Col and AGO10 OE S1. (XLSX)

Successful male gametogenesis involves orchestration of sequential gene regulation for somatic differentiation in pre-meiotic anthers. We report here the cloning of Male Sterile23 (Ms23), encoding an anther-specific predicted basic helix-loop-helix (bHLH) transcription factor required for tapetal differentiation; transcripts localize initially to t...

RNAi is a highly conserved machinery in eukaryotes for transcriptional or post-transcriptional silencing. In plants, RNA-directed DNA Methylation (RdDM) pathway deploys small interfering RNAs (siRNAs) to target DNA methylation. This process is initiated by the plant-specific RNA polymerase IV (Pol IV) to produce RNA precursors that are later proces...

Significance There are two main groups of land plants, flowering plants (also referred to as angiosperms) and gymnosperms. Compared with angiosperms, gymnosperms have larger genomes, often approximately 20 Gb, and have a higher abundance of transposons and other repetitive elements that are silenced by DNA methylation. Here, we present a whole geno...

DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me). To further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM...

Supplementary Figures 1 - 10, Supplementary Tables 1 - 3 and Supplementary References 1 - 3

TEs differentialy expressed in mthfd1-1

PCGs differentialy expressed in mthfd1-1

Significance Plant traits exhibit variation as a result of genetic and epigenetic change. Genetic variation is used for breeding and crop improvement. Epigenetic variation, especially differences in DNA methylation, also contributes to phenotype. For example, epigenetic alleles of plant genes exist in nature, which are identical in DNA sequence, bu...

Three soybean [Glycine max (L) Merr.] small RNA libraries were generated and sequenced using the Illumina platform to examine the role of miRNAs during soybean nodulation. The small RNA libraries were derived from root hairs inoculated with Bradyrhizobium japonicum (In_RH) or mock-inoculated with water (Un_RH), as well as from the comparable inocul...

3' uridylation is increasingly recognized as a conserved RNA modification process associated with RNA turnover in eukaryotes. 2'-O-methylation on the 3' terminal ribose protects micro(mi)RNAs from 3' truncation and 3' uridylation in Arabidopsis. Previously, we identified HESO1 as the nucleotidyl transferase that uridylates most unmethylated miRNAs...

Disease-related genes, particularly the nucleotide binding site (NB)–leucine-rich repeat (LRR) class of R plant genes can be triggered by microRNAs (miRNAs) to generate phased small interfering RNAs (phasiRNAs), which could reduce the transcript levels of their targets. However, how global changes in NB-LRR transcript levels coordinate with changes...

Plant microRNAs (miRNAs) play important regulatory roles in a number of developmental processes. The present work investigated the roles of miRNAs during nodule development in the crop legume soybean (Glycine max). Fifteen soybean small RNA libraries were sequenced from different stages of nodule development, including young nodules, mature nodules...

Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed from mRNA forming stem-loops; and (2) small interfering RNAs (siRNAs), the latter derived in plants by a process typically requiring an RNAdependent RNA polymerase. We constructed and analyzed an expression atlas of soybean (Glycine max) small RNAs, identi...

Chromosomes form 3D structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. Our genome-wide approach confirmed interactions that were previously observed by other methods as well as uncovered long-range interactions such as those amo...

Despite rapid doubling time, simple architecture and ease of metabolic labelling, a lack of genetic tools in the Lemnaceae (duckweed) has impeded the full implementation of this organism as a model for biological research. Here, we present technologies to facilitate high-throughput genetic studies in duckweed. We developed a fast and efficient meth...

The genus Phytophthora consists of many notorious pathogens of crops and forestry trees. To date, battling Phytophthora diseases is challenged by a lack of understanding on the pathogenesis. We investigated the role of small RNAs in regulating soybean defense in response to infection by Phytophthora sojae, the second most destructive pathogen of so...

In plants, post-transcriptional gene silencing (PTGS) is mediated by DICER-LIKE 1 (DCL1)-dependent microRNAs (miRNAs), which also trigger 21-nucleotide secondary short interfering RNAs (siRNAs) via RNA-DEPENDENT RNA POLYMERASE 6 (RDR6), DCL4 and ARGONAUTE 1 (AGO1), whereas transcriptional gene silencing (TGS) of transposons is mediated by 24-nucleo...

Significance The functional relationship of transposons and small RNAs remains an important question in the study of gene expression and its effect on agronomic traits. Here, we use deep sequencing of small RNAs to provide the first evidence that the rice Dicer-like 3 homolog OsDCL3a produces 24-nt small interfering RNAs (siRNAs) predominantly asso...

The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global...

Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication...

MicroRNAs (miRNAs) derive from longer precursors with fold-back structures. While animal miRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach to systematically analyze miRNA processing intermediates and characterize the biogenesis of most of the e...

MicroRNAs (miRNAs) are ∼21 nt small RNAs that pair to their target mRNAs and in many cases trigger cleavage, particularly in plants. Although many computational tools can predict miRNA:mRNA interactions, it remains critical to validate cleavage events, due to miRNA function in translational repression or due to high rates of false positives (over 9...

MicroRNAs (miRNAs) are a class of small RNAs which typically function by guiding cleavage of target messenger RNAs. They have been shown to play major roles in a variety of plant processes including development, and responses to pathogens and environmental stresses. To identify new miRNAs and regulation in Arabidopsis thaliana, 27 small RNA librari...

Background The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide. Endogenous small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs) are critical components of gene regulation in many eukaryotic organisms. Recently several new spec...

microRNAs (miRNAs) function via targeting of messenger RNAs, suppressing protein levels, and playing important roles in biological processes of plants and animals. The pathway for miRNA biogenesis is well established, but less is known about miRNA turnover, largely because of difficulties in capturing miRNAs during the process of decay, in which th...

In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (RNAP), RNAP IV and RNAP V. RNAP IV plays a major role in siRNA biogenesis, while RNAP V may recruit DNA methylation machin...

MicroRNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs) impact numerous biological processes in eukaryotes. In addition to biogenesis, turnover contributes to the steady-state levels of small RNAs. One major factor that stabilizes miRNAs and siRNAs in plants as well as siRNAs and piRNAs in animals is 2'-O-methylation...

Higher plants have evolved multiple proteins in the RNase III family to produce and regulate different classes of small RNAs with specialized molecular functions. In rice (Oryza sativa), numerous genomic clusters are targeted by one of two microRNAs (miRNAs), miR2118 and miR2275, to produce secondary small interfering RNAs (siRNAs) of either 21 or...

Small RNAs have a variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify previously unknown rice (Oryza sativa) microRNAs (miRNAs) and those regulated by environmental stress, 62 small RNA libraries...

Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymb...

Plant microRNAs (miRNAs) and small interfering RNAs (siRNAs) bear a 2'-O-methyl group on the 3'-terminal nucleotide. This methyl group is post-synthetically added by the methyltransferase protein HEN1 and protects small RNAs from enzymatic activities that target the 3'-OH. A mutagenesis screen for suppressors of the partial loss-of-function hen1-2...

Cytosine methylation is a common DNA modification found in most eukaryotic organisms including plants, animals, and fungi (1, 2). The addition of a methyl group to cytosine nucleotides in DNA does not change the primary DNA sequence, but the covalent modification of DNA by methylation can impact gene expression and activity in a heritable fashion....

Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenc...

Several recent analyses of plant microRNA precursors define the contributions of secondary structure to the precise positions at which processing of these precursors occurs.

Cosuppression is a classical form of eukaryotic post-transcriptional gene silencing. It was first reported in transgenic petunia, where a sense transgene meant to overexpress the host Chalcone Synthase-A (CHS-A) gene caused the degradation of the homologous transcripts and the loss of flower pigmentation. In this work, we used deep sequencing techn...

Gene silencing is a useful technique for elucidating biological function of genes by knocking down their expression. Recently developed artificial microRNAs (amiRNAs) exploit an endogenous gene silencing mechanism that processes natural miRNA precursors to small silencing RNAs that target transcripts for degradation. Based on natural miRNA structur...

The technological advances in DNA sequencing over the past five years have changed our approaches to gene expression analysis, fundamentally altering the basic methods used and in most cases driving a shift from hybridization-based approaches to sequencing-based approaches. Quantitative, tag-based studies of gene expression were one of the earliest...

Regulatory small RNAs (approximately 20 to 24nt in length) are produced through pathways that involve several key evolutionarily conserved protein families; the variants of these proteins found in plants are encoded by multigene families and are known as Dicer-like, Argonaute, and RNA-dependent RNA polymerase proteins. Small RNAs include the well-k...

Human PROTEIN ARGININE METHYLTRANSFERASE5 (PRMT5) encodes a type II protein arginine (Arg) methyltransferase and its homologs in animals and yeast (Saccharomyces cerevisiae and Schizosaccharomyces pombe) are known to regulate RNA processing, signal transduction, and gene expression. However, PRMT5 homologs in higher plants have not yet been reporte...

Although the role of H3K9 methylation in rice (Oryza sativa) is unclear, in Arabidopsis thaliana the loss of histone H3K9 methylation by mutation of Kryptonite [also known as SU(VAR)3-9 homolog] reduces genome-wide DNA methylation and increases the transcription of transposable elements. Here, we report that rice SDG714 (for SET Domain Group Protei...