摘要
ABSTRACT Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biologi- cal processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs （im-ncRNAs） （50-300 nt） have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half （58%） are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5＇-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited signifi- cantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epige- netic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.
ABSTRACT Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biologi- cal processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs （im-ncRNAs） （50-300 nt） have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half （58%） are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5＇-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited signifi- cantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epige- netic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.
基金
grants from the National Basic Research Program of China (973 Program)，the National Natural Science Foundation of China，in part by the Peking-Tsinghua Center for Life Sciences and a grant from the Next-Generation BioGreen 21 Program，Rural Development Administration,Republic of Korea
