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Introduction
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Publications
Publications (28)
Summary: Creation of Circos plot is one of the most efficient approaches to visualize genomic data. However, the installation and use of existing tools to make Circos plot are challenging for users lacking of coding experiences. To address this issue, we developed an R/Shiny application shinyCircos, a graphical user interface for interactive creati...
Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes. Currently, there is no specialized graphical user interface (GUI) designed to produce non-circular whole genome diagrams, and the use of existing tools requires considerable coding effort from users. Moreover, such tools also require impro...
A chromatin-based, RNA interference (RNAi)-independent mechanism re-establishes DNA methylation on heterochromatic transposable elements that lost silent marks in previous generations. Multiple factors including CG methylation and H2A.W replacement influence the efficiency of this methylation reprogramming mechanism.
DNA methylation in the non-CG context is widespread in the plant kingdom and abundant in mammalian tissues such as the brain and pluripotent cells. Non-CG methylation in Arabidopsis thaliana is coordinately regulated by DOMAINS REARRANGED METHYLTRANSFERASE (DRM) and CHROMOMETHYLASE (CMT) proteins but has yet to be systematically studied in major cr...
In the eukaryotic nucleus, heterochromatin forms highly condensed, visible foci known as heterochromatin foci (HF). These HF are enriched with linker histone H1, a key player in heterochromatin condensation and silencing. However, it is unknown how H1 aggregates HF and condenses heterochromatin. In this study, we established that H1 facilitates het...
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....
High-throughput RNA-sequencing (RNA-seq) has become the most popular technology for profiling gene expression in the last decade due to its low cost and high coverage. As a result, the number of RNA-seq libraries from the plant community has been increasing exponentially in recent years. For major crops, such as maize, rice, soybean, wheat, and cot...
In the past decade, genome-wide characterization of the three-dimensional chromatin structure in plants using high-throughput methods has greatly advanced our knowledge in plant genome architecture (Liu and Weigel, 2015; Ouyang et al., 2020). However, due to the limitation of Illumina short-read sequencing, the genome-wide contact map obtained by H...
Background
The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods.
Results
Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Ara...
In plants, small RNAs (sRNAs) that are 22 nucleotides (nt) in length have the unique capacity to trigger the production of secondary small interfering RNAs (siRNAs) and further enhance silencing. While DCL2-dependent 22-nt siRNAs are rare in Arabidopsis and thought to have few functions except during viral infection, they are abundant in many major...
Precise mapping of quantitative trait loci (QTLs) is critical for assessing the genetic effects and identification of candidate genes for quantitative traits. Interval and composite interval mappings have been the methods of choice for several decades, which have provided tools for identifying genomic regions harboring causal genes for quantitative...
The ubiquitin 26S proteasome system (UPS) is critical for enabling plants to alter their proteomes to integrate internal and external signals for the photoperiodic induction of flowering. We previously demonstrated that HAF1, a C3HC4 RING domain-containing E3 ubiquitin ligase, is essential to precisely modulate the timing of Heading Date1 accumulat...
Background: As a main staple food, rice is also a model plant for functional genomic studies of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and prope...
In rice (Oryza sativa L.), hybrids between indica and japonica subspecies are usually highly sterile, which provides a model system for studying postzygotic reproductive isolation. A killer-protector system S5 composed of three adjacent genes, ORF3, ORF4 and ORF5, regulates female gamete fertility of indica-japonica hybrids. To characterize the pro...