Qin, E. | Search bioRxiv

bioRxiv2022

OUGene 2.0: An updated disease-associated over- and under-expressed gene database by mining full-text articles

Many diseases are closely associated with over- or under-expressed genes. In order to cover more up to date associations between over- or under-expressed genes and various diseases, we develop an updated database OUGENE 2.0 for disease-associated over- and under-expressed genes by automatic full-text mining. In total, the new OUGene 2.0 includes 197,236 associations between 12,672 diseases and 11,542 over- or under-expressed genes, which increases by about 5 folds compared to the previous version of OUGene. A novel method for rescaling the raw score based on support evidences is designed to prioritize the mined associations. OUGene 2.0 provides a holistic view of disease-gene associations and it supports user-friendly data exploration at www.csbio.sjtu.edu.cn/bioinf/OUGene for academic use.

bioinformatics↗

bioRxiv2020

Heat Stress Interferes with Formation of Double-Strand Breaks and Homology Synapsis in Arabidopsis thaliana

Meiotic recombination (MR) drives novel combination of alleles and contributes to genomic diversity in eukaryotes. In this study, we showed that heat stress (36-38{degrees}C) over fertile threshold fully abolished crossover (CO) formation in Arabidopsis. Cytological and genetic studies in wild-type plants, and the syn1 and rad51 mutants suggested that heat stress reduces generation of SPO11-dependent double-strand breaks (DSBs). In support, the abundance of recombinase DMC1, which is required for MR-specific DSB repair, was significantly reduced under heat stress. In addition, we showed that high temperatures induced disassembly and/or instability of ASY4-but not SYN1-mediated chromosome axis. At the same time, ASY1-associated lateral element of synaptonemal complex (SC) was partially affected, while the ZYP1-dependent central element of SC was disrupted, indicating that heat stress impairs SC formation. Moreover, quantitative RT-PCR revealed that genes involved in DSB formation; e.g. SPO11-1, PRD1, 2 and 3, were not impacted; however, recombinase RAD51 and chromosome axis factors ASY3 and ASY4 were significantly downregulated under heat stress. Taken together, these findings revealed that heat stress inhibits MR via compromised DSB formation and homolog synapsis, which are possible downstream effects of the impacted chromosome axis. Our study thus provides evidence shedding light on how increase of environmental temperature influences MR in Arabidopsis.

plant biology↗