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
Genome-wide cis-decoding for expression design in tomato using cistrome data and explainable deep learning
Abstract: In the evolutionary history of plants, variation in cis-regulatory elements (CREs) resulting in diversification of gene expression has played a central role in driving the evolution of lineage-specific traits....
OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice
Abstract: Grains from cereals contribute an important source of protein to human food, and grain protein content (GPC) is an important determinant of nutritional quality in cereals. Here we show...
H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction
Abstract: Nearly 50% of mouse and human genomes are composed of repetitive sequences. Transcription of these sequences is tightly controlled during development to prevent genomic instability, inappropriate gene activation and...
Splicing-mediated activation of SHAGGY-like kinases underpinning carbon partitioning in Arabidopsis seeds
Abstract: Glycogen synthase kinase 3 (GSK3) family members serve as signaling hubs for plant development and stress responses, yet the underlying mechanism of their transcriptional regulation remains a long-standing mystery....
Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa
Abstract: Long non-coding RNAs (lncRNAs) are emerging as versatile regulators in diverse biological processes. How- ever, little is known about their cis- and trans-regulatory contributions in gene expression under salt...
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation
Abstract: Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of reg- ulatory elements is fundamental for annotating genomes and...
Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation
Abstract: High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to...
DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development
Abstract: A contribution of DNA methylation to defense against invading nucleic acids and maintenance of genome integrity is uncontested; however, our understanding of the extent of involvement of this epigenetic...
