Bioinformatic approaches of liquid-liquid phase separation in human disease

Biomolecular aggregation within cellular environments via liquid-liquid phase separation(LLPS)spontaneously forms droplet-like structures,which play pivotal roles in diverse biological processes.These structures are closely associated with a range of diseases,including neurodegenerative disorders,cancer and infectious diseases,highlighting the significance of understanding LLPS mechanisms for elucidating disease pathogenesis,and exploring potential therapeutic interventions.In this review,we delineate recent advancements in LLPS research,emphasizing its pathological relevance,therapeutic considerations,and the pivotal role of bioinformatic tools and databases in facilitating LLPS investigations.Additionally,we undertook a comprehensive analysis of bioinformatic resources dedicated to LLPS research in order to elucidate their functionality and applicability.By providing comprehensive insights into current LLPS-related bioinformatics resources,this review highlights its implications for human health and disease.

Comprehensive landscape of resistance mechanisms for neoadjuvant therapy in esophageal squamous cell carcinoma by single-cell transcriptomics

Dear Editor,Preoperative neoadjuvant therapy combined with surgical resection is the standard treatment for locally advanced esopha-geal squamous cell carcinoma(ESCC).However,more than half of patients having a partial response to neoadjuvant therapy,which is considered as a therapy-resistant phenotype and the mechan-ism is still unclear.The heterogeneity of the ESCC with surgery alone therapy were characterized by single-cell RNA sequencing(scRNA-seq)previously,but few report was about ESCC patients with neoadjuvant therapy.1 It is emergent to illustrate the comprehensive hallmarks of neoadjuvant therapy-resistance in ESCC at single cell level.

Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells

Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica （93-11 ） and japonica （Nipponbare） inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By con- trast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-of- origin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9acJH3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells.

Transcriptome Survey of the Contribution of Alternative Splicing to Proteome Diversity in Arabidopsis thaliana

Dear Editor, Alternative splicing （AS） functions as a key regulatory mechanism and increases transcriptome and proteome diversity. Recent genome-wide studies have substantially expanded our estimation of the frequency of AS in plants （Reddy et al., 2013; Staiger and Brown, 2013）. However, the proportion of AS events that lead to increased proteome diversity in plants, rather than imperfect Dre-mRNA processing. remains unsolved. Here.