Software
Chorus2
Design of genome-scale oligonucleotide-based probes for fluorescence in situ hybridization (FISH)
CRISPR-BETS
A gRNA design software for base editing knockout using stop codon.
Popera
A software specially designed for DHS identification. Github Introduction DNase I hypersensitive sites (DHSs) are regions of chromatin that are sensitive to cleavage by the...
Latest
Chorus2 oligo datasets
Oligo datasets which host oligo sequences for Oligo-FISH. Details Introduction The oligo datasets currently host oligo sequences of nine species, including Arabidopsis, rice, maize, potato, barley, soybean, human, mouse and...
PlantDHS
PlantDHS: a database for DNase I hypersensitive sites (DHSs) in plants.
Lab meeting
Report: Integrated global analysis reveals a vitamin E- vitamin K1 sub-network, downstream of COLD1, underlying rice chilling tolerance divergence
Abstract: Rice, a staple food with tropical/subtropical origination, is susceptible to cold stress, one of the major con- straints on its yield and distribution. Asian cultivated rice consists of two...
Report: The Taxus genome provides insights into paclitaxel biosynthesis
Abstract: The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We...
Report: In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants
Abstract: Background: mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites,...
Report: Determinants of genome-wide distribution and evolution of uORFs in eukaryotes
Abstract: Upstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood....
Report: Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity
Abstract: Human dendritic cells (DCs) comprise subsets with distinct phenotypic and functional characteristics, but the transcriptional programs that dictate their identity remain elusive. Here, we analyze global chromatin acces- sibility...
Report: Natural variations of SLG1 confer high-temperature tolerance in indica rice
Abstract: With global warming and climate change, breeding crop plants tolerant to high-temperature stress is of immense significance. tRNA 2-thiolation is a highly conserved form of tRNA modification among living...
Report: Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression
Abstract: Pinpointing functional noncoding DNA sequences and defining their contributions to health-related traits is a major challenge for modern genetics. We developed a high-throughput framework to map noncoding DNA functions...
Report: Chromothripsis as an on-target consequence of CRISPR–Cas9 genome editing
Abstract: Genome editing has therapeutic potential for treating genetic diseases and cancer. However, the currently most practicable approaches rely on the generation of DNA double-strand breaks (DSBs), which can give...
Report: Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators
Abstract: Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in...
Report: A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes
Abstract: Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here,...
Report: Unidirectional movement of small RNAs from shoots to roots in interspecific heterograf
Abstract: Long-distance RNA movement is important for plant growth and environmental responses; however, the extent to which RNAs move between distant tissues, their relative magnitude and functional importance remain to...
Report: G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice
Abstract: The simultaneous improvement of grain quality and yield of cereal crops is a major challenge for modern agriculture. Here we show that a rice grain yield quantitative trait locus...
Report: Molecular Networks of Seed Size Control in Plants
Abstract: The size of seeds affects not only evolutionary fitness but also grain yield of crops. Understanding the mechanisms controlling seed size has become an important research field in plant...
Report: Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco Leaves
Abstract: Genetic engineering of cis-regulatory elements in crop plants is a promising strategy to ensure food security. However, such engineering is currently hindered by our limited knowledge of plant cis-regulatory...
Report: Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis
Abstract: Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions...
Report: Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis
Abstract: Plant somatic embryogenesis refers to a phenomenon where embryos develop from somatic cells in the absence of fertilization. Previous studies have revealed that the phytohormone auxin plays a crucial...
