Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants

RNA secondary structure plays a critical role in gene regulation. Rice （Oryza sativa） is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, we have successfully generated in vivo Structure-seq libraries in rice. We found that the structural flexibility of mRNAs might associate with the dynamics of biological function. Higher N6-methyladenosine （mSA） modification tends to have less RNA structure in 3＇ UTR, whereas GC content does not significantly affect in vivo mRNA structure to maintain efficient biological processes such as translation. Comparative analysis of RNA structurome between rice and Arabidopsis revealed that higher GC content does not lead to stronger structure and less RNA structural flexibility. Moreover, we found a weak correlation between sequence and structure conservation of the orthologs between rice and Arabidopsis. The conservation and divergence of both sequence and in vivo RNA structure corresponds to diverse and specific biological processes. Our results indicate that RNA secondary structure might offer a separate layer of selection to the sequence between monocot and dicot. Therefore, our study implies that RNA structure evolves differently in various biological processes to maintain robustness in development and adaptational flexibility during angiosperm evolution.

RiceENCODE:A comprehensive epigenomicdatabase as a rice Encyclopedia of DNA Elements

Dear Editor,Rice(Oryza sativa)is one of the most important crops in the worldand a common model plant for genomic research.The genomesofXian/IndicaandGeng/Japonicahave been completelysequenced and annotated with accurate genome information.Over the past few years,epigenomic information,including DNAmethylation,histone modification,and chromatin accessibility,has been characterized in theXian/IndicaandGeng/Japonicage-nomes(Zhao et al.,2020).Quite a few rice three-dimensionalgenome studies have been published in the meantime(Zhaoet al.,2019).However,it is still a big challenge for many groupsthat lack dedicated bioinformatic personnel or sufficientcomputational resources to utilize such epigenetic data.

HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancer

Integration of human papillomavirus(HPV)DNA into the human genome is a reputed key driver of cervical cancer.However,the effects of HPV integration on chromatin structural organization and gene expression are largely unknown.We studied a cohort of 61 samples and identified an integration hot spot in the CCDC106 gene on chromosome 19.We then selected fresh cancer tissue that contained the unique integration loci at CCDC106 with no HPV episomal DNA and performed whole-genome,RNA,chromatin immunoprecipitation and high-throughput chromosome conformation capture(Hi-C)sequencing to identify the mechanisms of HPV integration in cervical carcinogenesis.Molecular analyses indicated that chromosome 19 exhibited significant genomic variation and differential expression densities,with correlation found between three-dimensional(3D)structural change and gene expression.Importantly,HPV integration divided one topologically associated domain(TAD)into two smaller TADs and hijacked an enhancer from PEG3 to CCDC106,with a decrease in PEG3 expression and an increase in CCDC106 expression.This expression dysregulation was further confirmed using 10 samples from our cohort,which exhibited the same HPV-CCDC106 integration.In summary,we found that HPV-CCDC106 integration altered local chromosome architecture and hijacked an enhancer via 3D genome structure remodeling.Thus,this study provides insight into the 3D structural mechanism underlying HPV integration in cervical carcinogenesis.

Bioinformatics approaches to analyzing CRISPR screen data:from dropout screens to single-cell CRISPR screens

Background:Pooled CRISPR screen is a promising tool in drug targets or essential genes identification with the utilization of three different systems including CRISPR knockout(CRISPRko),CRISPR interference(CRISPRi)and CRISPR activation(CRISPRa).Aside from continuous improvements in technology,more and more bioinformatics methods have been developed to analyze the data obtained by CRISPR screens which facilitate better understanding of physiological effects.Results:Here,we provide an overview on the application of CRISPR screens and bioinformatics approaches to analyzing different types of CRISPR screen data.We also discuss mechanisms and underlying challenges for the analysis of dropout screens,sorting-based screens and single-cell screens.Conclusion:Different analysis approaches should be chosen based on the design of screens.This review will help community to better design novel algorithms and provide suggestions for wet-lab researchers to choose from different analysis methods.