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
Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq
Abstract: Embryonic stem cells (ESCs) can differentiate into any given cell type and therefore represent a versatile model to study the link between gene regulation and differentiation. To quantitatively assess...
Quantitative regulation of Waxy expression by CRISPR/Cas9-based promoter and 5’UTR-intron editing improves grain quality in rice
Abstract: In cereal crops, grain starches are composed of different proportions of amylose and amylopectin, which determine the cooking and eating qualities. The amylose synthesis is controlled by the Waxy...
Nucleolar histone deacetylases HDT1, HDT2 and HDT3 regulate plant reproductive development
Abstract: Nucleolus is a membrane-less organelle where ribosomes are assembled and rRNAs transcribed and processed. The assembled ribosomes composed of ribosomal proteins and rRNAs synthesize proteins for cell survival. In...
Plastidic Pyruvate Dehydrogenase Complex E1 Component Subunit Alpha1 Is Involved in Galactolipid Biosynthesis Required for Amyloplast Development in Rice
Abstract: Starch accounts for over 80% of the total dry weight in cereal endosperm and determines the kernel texture and nutritional quality. Amyloplasts, terminally differentiated plastids, are responsible for starch...
Organization and regulation of gene transcription
Abstract: The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and...
A photoregulatory mechanism of the circadian clock in Arabidopsis
Abstract: Cryptochromes (CRYs) are photoreceptors that mediate light regulation of the circadian clock in plants and animals. Here we show that CRYs mediate blue-light regulation of N6-methyladenosine (m6A) modification of...
Report: MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities
Abstract: MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5...
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: Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish
Abstract: Sight depends on the tight cooperation between photoreceptors and pigmented cells, which derive from common progenitors through the bifurcation of a single gene regulatory network into the neural retina...
