Phased small interfering RNAs(phasiRNAs) are abundantly expressed in anthers and linked to environment-related male fertility in grasses, yet how they function under different environmental conditions remains unclear....Phased small interfering RNAs(phasiRNAs) are abundantly expressed in anthers and linked to environment-related male fertility in grasses, yet how they function under different environmental conditions remains unclear. Here, we identified a rice(Oryza sativa) low temperature-induced Argonaute(AGO) protein, OsAGO1d, that is responsible for generating phasiRNAs and preserving male fertility at low temperature. Loss of OsAGO1d function causes low-temperature male sterility associated with delayed programmed cell death of tapetal cells during anther development. OsAGO1d binds miR2118 and miR2275 family members and triggers phasiRNA biogenesis;it also binds 21-nt phasiRNAs with a 5′ terminal U. In total, phasiRNAs from 972loci are OsAGO1d-dependent. OsAGO1d protein moves from anther wall cells into meiocytes, where it loads miR2275 to produce 24-nt phasiRNAs. Together, our results show that OsAGO1d acts as a mobile signal to fine-tune phasiRNA production and this function is important for male fertility at low temperature.展开更多
Recent studies have indicated that a special type of small noncoding RNAs, phased small-interfering RNAs(phasiRNAs) play crucial roles in many cellular processes of plant development. PhasiRNAs are generated from long...Recent studies have indicated that a special type of small noncoding RNAs, phased small-interfering RNAs(phasiRNAs) play crucial roles in many cellular processes of plant development. PhasiRNAs are generated from long RNA precursors at intervals of 21 or 24 nt in plants, and they are produced from both protein-coding gene and long noncoding RNA genes. Different from those in eudicots, grass phasiRNAs include a special class of small RNAs that are specifically expressed in reproductive organs.These grass phasiRNAs are associated with gametogenesis, especially with anther development and male fertility. In this review,we summarized current knowledge on these small noncoding RNAs in male germ cells and their possible biological functions and mechanisms in grass species.展开更多
Small RNAs(sRNAs),found extensively in plants,play an essential role in plant growth and development.Although various sRNA analysis tools have been developed for plants,the use of most of them depends on programming a...Small RNAs(sRNAs),found extensively in plants,play an essential role in plant growth and development.Although various sRNA analysis tools have been developed for plants,the use of most of them depends on programming and command-line environments,which is a challenge for many wet-lab biologists.Furthermore,current sRNA analysis tools mostly focus on the analysis of certain type of sRNAs and are resource-intensive,normally demanding an immense amount of time and effort to learn the use of numerous tools or scripts and assemble them into a workable pipeline to get the final results.Here,we present sRNAminer,a powerful stand-alone toolkit with a user-friendly interface that integrates all common functions for the analysis of three major types of plant sRNAs:microRNAs(miRNAs),phased small interfering RNAs(phasiRNAs),and heterochromatic siRNAs(hc-siRNAs).We constructed a curated or"golden"set of MIRNA and PHAS loci,which was used to assess the performance of sRNAminer in comparison to other existing tools.The results showed that sRNAminer outperformed these tools in multiple aspects,highlighting its functionality.In addition,to enable an efficient evaluation of sRNA annotation results,we developed Integrative Genomics Viewer(IGV)-sRNA,a modified genome browser optimized from IGV and we incorporated it as a functional module in sRNAminer.IGV-sRNA can display a wealth of sRNA-specific features,enabling a more comprehensive understanding of sRNA data.sRNAminer and IGV-sRNA are both platform-independent software that can be run under all operating systems.They are now freely available at https://github.com/kli28/sRNAminer and https://gitee.com/CJchen/IG V-sRNA.展开更多
Small RNAs(sRNAs) are vital regulators of gene expression and involved in various biological processes. Among them, micro RNAs(mi RNAs) and phased small interfering RNAs(phasi RNAs) have been well defined and studied ...Small RNAs(sRNAs) are vital regulators of gene expression and involved in various biological processes. Among them, micro RNAs(mi RNAs) and phased small interfering RNAs(phasi RNAs) have been well defined and studied in the past decades. A bunch of scripts or pipelines were developed to annotate mi RNAs and phasi RNAs. However, some computational annotations are rough and without careful manual check,resulting in low quality annotation. In this study, 19 public strawberry(Fragaria vesca) s RNA sequencing data from nine different tissues were collected to annotate mi RNAs and PHAS loci in F. vesca. After bioinformatics analysis and careful manual checking, 167 known mi RNAs, 27 mi RNA*s with notable abundance, 54 novel mi RNAs were accurately annotated. The terms of two mi RNAs were corrected from mi R477 b and mi R5225 using mi RN47 and mi R3627 h, respectively. Besides 21 nucleotides(nt) mi R390, eleven mi RNAs with a length of 22-nt are in charge of triggering the biogenesis of 21-nt phasi RNAs from 110 PHAS loci in strawberry. In particular, we found several PHAS loci were targeted by two different mi RNAs(similar to the "two-hit" model) and the phasi RNA generating region located between two target sites. We speculate that one target site is in control of triggering phasi RNA biogenesis and the other target site define the boundary of the region of phasi RNA biogenesis,which likely provide an accurate way for phasi RNA generation. Overall, we provided a comprehensive and accurate annotation of mi RNAs and PHAS loci in the F. vesca genome.展开更多
基金supported by the National Natural Science Foundation of China(31788103,32170620)the Chinese Academy of Sciences(QYZDY-SSW-SMC022,XDB27030201,XDA24010302)the State Key Laboratory of Plant Genomics。
文摘Phased small interfering RNAs(phasiRNAs) are abundantly expressed in anthers and linked to environment-related male fertility in grasses, yet how they function under different environmental conditions remains unclear. Here, we identified a rice(Oryza sativa) low temperature-induced Argonaute(AGO) protein, OsAGO1d, that is responsible for generating phasiRNAs and preserving male fertility at low temperature. Loss of OsAGO1d function causes low-temperature male sterility associated with delayed programmed cell death of tapetal cells during anther development. OsAGO1d binds miR2118 and miR2275 family members and triggers phasiRNA biogenesis;it also binds 21-nt phasiRNAs with a 5′ terminal U. In total, phasiRNAs from 972loci are OsAGO1d-dependent. OsAGO1d protein moves from anther wall cells into meiocytes, where it loads miR2275 to produce 24-nt phasiRNAs. Together, our results show that OsAGO1d acts as a mobile signal to fine-tune phasiRNA production and this function is important for male fertility at low temperature.
基金supported by the National Natural Science Foundation of China (91640202, 91335104)the grants from Guangdong Province (2016A030308015) and Guangzhou (201707020018, 201710010029)
文摘Recent studies have indicated that a special type of small noncoding RNAs, phased small-interfering RNAs(phasiRNAs) play crucial roles in many cellular processes of plant development. PhasiRNAs are generated from long RNA precursors at intervals of 21 or 24 nt in plants, and they are produced from both protein-coding gene and long noncoding RNA genes. Different from those in eudicots, grass phasiRNAs include a special class of small RNAs that are specifically expressed in reproductive organs.These grass phasiRNAs are associated with gametogenesis, especially with anther development and male fertility. In this review,we summarized current knowledge on these small noncoding RNAs in male germ cells and their possible biological functions and mechanisms in grass species.
基金supported by the National Natural Science Foundation of China(32072547 and 32102320)the Key-Area Research and Development Program of Guangdong Province(2022B0202070003)+2 种基金supported by the open competition program of top 10 critical priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province(2022SDZG05)the Hainan Yazhou Bay Seed Lab(JBGS-B21HJ0001)the Meyers lab on small RNA classification and miRNA annotation is supported by US National Science Foundation Award(2130883)。
文摘Small RNAs(sRNAs),found extensively in plants,play an essential role in plant growth and development.Although various sRNA analysis tools have been developed for plants,the use of most of them depends on programming and command-line environments,which is a challenge for many wet-lab biologists.Furthermore,current sRNA analysis tools mostly focus on the analysis of certain type of sRNAs and are resource-intensive,normally demanding an immense amount of time and effort to learn the use of numerous tools or scripts and assemble them into a workable pipeline to get the final results.Here,we present sRNAminer,a powerful stand-alone toolkit with a user-friendly interface that integrates all common functions for the analysis of three major types of plant sRNAs:microRNAs(miRNAs),phased small interfering RNAs(phasiRNAs),and heterochromatic siRNAs(hc-siRNAs).We constructed a curated or"golden"set of MIRNA and PHAS loci,which was used to assess the performance of sRNAminer in comparison to other existing tools.The results showed that sRNAminer outperformed these tools in multiple aspects,highlighting its functionality.In addition,to enable an efficient evaluation of sRNA annotation results,we developed Integrative Genomics Viewer(IGV)-sRNA,a modified genome browser optimized from IGV and we incorporated it as a functional module in sRNAminer.IGV-sRNA can display a wealth of sRNA-specific features,enabling a more comprehensive understanding of sRNA data.sRNAminer and IGV-sRNA are both platform-independent software that can be run under all operating systems.They are now freely available at https://github.com/kli28/sRNAminer and https://gitee.com/CJchen/IG V-sRNA.
基金supported by the National Natural Science Foundation of China(Grant No.31872063)。
文摘Small RNAs(sRNAs) are vital regulators of gene expression and involved in various biological processes. Among them, micro RNAs(mi RNAs) and phased small interfering RNAs(phasi RNAs) have been well defined and studied in the past decades. A bunch of scripts or pipelines were developed to annotate mi RNAs and phasi RNAs. However, some computational annotations are rough and without careful manual check,resulting in low quality annotation. In this study, 19 public strawberry(Fragaria vesca) s RNA sequencing data from nine different tissues were collected to annotate mi RNAs and PHAS loci in F. vesca. After bioinformatics analysis and careful manual checking, 167 known mi RNAs, 27 mi RNA*s with notable abundance, 54 novel mi RNAs were accurately annotated. The terms of two mi RNAs were corrected from mi R477 b and mi R5225 using mi RN47 and mi R3627 h, respectively. Besides 21 nucleotides(nt) mi R390, eleven mi RNAs with a length of 22-nt are in charge of triggering the biogenesis of 21-nt phasi RNAs from 110 PHAS loci in strawberry. In particular, we found several PHAS loci were targeted by two different mi RNAs(similar to the "two-hit" model) and the phasi RNA generating region located between two target sites. We speculate that one target site is in control of triggering phasi RNA biogenesis and the other target site define the boundary of the region of phasi RNA biogenesis,which likely provide an accurate way for phasi RNA generation. Overall, we provided a comprehensive and accurate annotation of mi RNAs and PHAS loci in the F. vesca genome.
