Genome-wide Identification And Characterization Of RBPs In Maize

Maize is the largest and most productive crop in China and the world,serving as an important source of feed for human food and farming,as well as an important industrial raw material.Maize originated in South and Central America and has gradually spread to various regions around the world and has strong environmental adaptability.In order to adapt to the environment of different regions of the world and the current complex and variable global climate,maize has developed complex expression regulation mechanisms.With the advent and continuous development of high-throughput sequencing technologies,especially transcriptomics,we have gained an in-depth understanding of maize transcriptome composition and regulatory networks.However,we still know very little about posttranscriptional regulation.RNA-binding proteins(RBPs)are important components of post-transcriptional regulation in plants.This study is intended to explore the molecular mechanisms of post-transcriptional regulation in maize based on the identification,characterization,and potential functions of maize genome-wide RBPs.Based on the isolation principle of RNA isolation from RBPs,we developed a new method genome-wide RBPs extraction(GW-RBPs-E)for the extraction of genome-wide RBPs in maize,and then explored the post-transcriptional regulatory mechanisms of maize RNAs.Using this method,we identified 2,672 RBPs with conserved RNA-binding domains(RBDs)in the leaves of maize inbred line B73.Meanwhile,we found that RBPs genes in maize are closely associated with the production of circular RNAs(circRNAs).Finally,we performed association of variation in different agronomic traits of maize based on the structural variation of genes that produce RBPs.Finally,our analysis revealed that a large number of RBPs genes regulate numerous trait variants,opening new perspectives for further understanding the molecular mechanisms of maize trait variation.The specific findings of this study are as follows.(1)This study adapted and optimized a new RBPs identification method,GW-RBPs-E,that can be applied in plants.It was developed based on the well-established RBP identification technique XRNAX in humans.By using this method,we identified 2,672 RBPs in the leaves of maize inbred line B73.these RBPs have conserved RBDs,which can be further classified into classical(116),nonclassical(143),and unknown(919)RBDs.GO analysis revealed that these RBP genes also show their regulatory functions in m RNA binding,RNA processing,transcription,and translation.(2)To further explore the functions of these RBPs,we performed the association analysis of these RBP genes for different agronomic traits in maize.Further analysis revealed that genomic structural variation associated with important agronomic traits was significantly enriched in the gene regions encoded by RBPs,which enriched the most abundant trait association signals for 100-grain weight,kernel width,and cob weight.(3)Previous studies have shown that RBPs may be involved in the formation of circular RNAs.In order to clarify the relationship between circRNAs and RBPs in maize,and to analyze the way RBPs function,we conducted co-localization and co-expression analysis on 1303 circRNAs identified in maize leaves and RBPs.The results showed that all 538 identified RBPs had a co-expression relationship with circRNAs,which was significantly lower than random;however,the expression abundance of host genes with 8478 circRNAs was significantly associated with RBPs,which was significantly higher than random.The results show that RBP in maize can regulate the formation of circular RNA by binding to host gene RNAIn this study,a new tool for identifying RBPs in plants(GW-RBPs-E),was developed to identify the number,genomic distribution,and other properties of leaf RBPs in maize,and to provide a preliminary exploration of the way they exercise their functions.This study is the first attempt of genome-wide identification and functional analysis of RBPs in maize and provides new ideas for further understanding the molecular mechanisms of agronomic trait variation in maize,which is of great reference value.