A5041119515- Plant Molecular Biology Research
- Chromosomal and Genetic Variations
- Plant nutrient uptake and metabolism
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Legume Nitrogen Fixing Symbiosis
- Plant Virus Research Studies
- Plant Disease Resistance and Genetics
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Plant-Microbe Interactions and Immunity
- Photosynthetic Processes and Mechanisms
- Plant Reproductive Biology
- Epigenetics and DNA Methylation
- Plant responses to water stress
- Plant tissue culture and regeneration
- CRISPR and Genetic Engineering
- Single-cell and spatial transcriptomics
- Advanced biosensing and bioanalysis techniques
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- Nanopore and Nanochannel Transport Studies
- RNA Interference and Gene Delivery
- Plant Stress Responses and Tolerance
Southern University of Science and Technology
2016-2025
Northwest A&F University
2025
University of California, Los Angeles
2014-2018
University of Delaware
2008-2017
Biotechnology Institute
2008-2017
State Key Laboratory of Plant Genomics
2007-2011
Institute of Genetics and Developmental Biology
2005-2011
Chinese Academy of Sciences
2005-2011
University of Chinese Academy of Sciences
2008
Foundation Center
2006
Amborella trichopoda is strongly supported as the single living species of sister lineage to all other extant flowering plants, providing a unique reference for inferring genome content and structure most recent common ancestor (MRCA) angiosperms. Sequencing genome, we identified an ancient duplication predating angiosperm diversification, without evidence subsequent, lineage-specific duplications. Comparisons between angiosperms facilitated reconstruction ancestral gene order in MRCA core...
Legumes and many nonleguminous plants enter symbiotic interactions with microbes, it is poorly understood how host respond to promote beneficial, microbial while suppressing those that are deleterious or pathogenic. Trans -acting siRNAs (tasiRNAs) negatively regulate target transcripts characterized by spaced in 21-nucleotide (nt) “phased” intervals, a pattern formed DICER-LIKE 4 (DCL4) processing. A search for phased (phasiRNAs) found at least 114 Medicago loci, the majority of which were...
Abstract 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, chromatin modification. To identify previously unknown rice (Oryza sativa) microRNAs (miRNAs) those regulated environmental stress, 62 small RNA libraries were constructed from plants used for deep sequencing with Illumina technology. The represent several tissues control subjected to different...
Summary 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 two microRNAs (miRNAs), miR2118 miR2275, secondary interfering (siRNAs) either 21 or 24 nucleotides a phased manner. The biogenesis requirements functions completely unknown. Here we examine Dicer‐Like (DCL) family, including OsDCL1, ‐3a, ‐3b ‐4. By...
Significance By RNA profiling of 10 stages maize anthers plus mature pollen, we found two distinct classes phased small-interfering RNAs (phasiRNAs): 21-nt premeiotic phasiRNAs, after germinal and somatic cell specification, 24-nt meiotic phasiRNAs coordinately accumulated during meiosis persist into pollen. Sequencing from five male-sterile, anther developmental mutants— ocl4 , mac1 ms23 msca1 ameiotic1 —demonstrated the involvement specific layers. Premeiotic require a functional...
Significance The functional relationship of transposons and small RNAs remains an important question in the study gene expression its effect on agronomic traits. Here, we use deep sequencing to provide first evidence that rice Dicer-like 3 homolog OsDCL3a produces 24-nt interfering (siRNAs) predominantly associated with miniature inverted repeat transposable elements (MITEs). These siRNAs target genes adjacent MITEs act as broadly functioning regulators expression. In particular, directly...
Dear Editor, High-throughput RNA-sequencing (RNA-seq) has become the most popular technology for profiling gene expression in last decade due to its low cost and high coverage. As a result, number of RNA-seq libraries from plant community been increasing exponentially recent years (Figure 1a). For major crops, such as maize, rice, soybean, wheat cotton, collected total ~45 000 by 2021 1b). Although currently there are several databases plants, example, CoNekT with 750 rice 574 maize...
Abstract Although the role of H3K9 methylation in rice (Oryza sativa) is unclear, Arabidopsis thaliana loss histone by mutation Kryptonite [also known as SU(VAR)3-9 homolog] reduces genome-wide DNA and increases transcription transposable elements. Here, we report that SDG714 (for SET Domain Group Protein714) encodes a H3K9-specific methyltransferase. The C terminus confers enzymatic activity substrate specificity, whereas N localizes it nucleus. Loss-of-function mutants (SDG714IR...
ArchPRED server (http://www.fiserlab.org/servers/archpred) implements a novel fragment-search based method for predicting loop conformations. The inputs to the are atomic coordinates of query protein and position loop. algorithm selects candidate fragments from regularly updated library (Search Space) by matching length, types bracing secondary structures satisfying geometrical restraints imposed stem residues. Subsequently, loops inserted in framework where their side chains rebuilt fit is...
Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed from mRNA forming stem-loops; (2) small interfering (siRNAs), the latter derived in plants by a process typically requiring an RNA-dependent RNA polymerase. We constructed analyzed expression atlas of soybean (Glycine max) RNAs, identifying over 500 loci generating 21-nucleotide phased siRNAs (phasiRNAs; PHAS loci), which 483 overlapped annotated protein-coding genes. Via integration miRNAs with...
DNA methylation is important for the regulation of gene expression and silencing transposons in plants. Here we present genome-wide patterns at single-base pair resolution cassava (Manihot esculenta, cultivar TME 7), a crop with substantial impact agriculture subtropical tropical regions. On average, levels were higher all three sequence contexts (CG, CHG, CHH, where H equals A, T, or C) than those most well-studied model plant Arabidopsis thaliana. As other plants, was found both on...
The genus Phytophthora consists of many notorious pathogens crops and forestry trees. At present, battling diseases is challenging due to a lack understanding their pathogenesis. We investigated the role small RNAs in regulating soybean defense response infection by sojae, second most destructive pathogen soybean. Small RNAs, including microRNAs (miRNAs) interfering (siRNAs), are universal regulators that repress target gene expression eukaryotes. identified known novel differentially...
MicroRNAs (miRNAs) derive from longer precursors with fold-back structures. While animal miRNA have homogenous structures, plant comprise a collection of fold-backs variable size and shape. Here, we design an approach to systematically analyze processing intermediates characterize the biogenesis most evolutionarily conserved miRNAs present in Arabidopsis thaliana . We found that are processed by four mechanisms, depending on sequential direction machinery number cuts required release miRNA....