Mechanisms of Small RNA Generation from Cis-NATs in Response to Environmental and Developmental Cues  

作　　者：Xiaoming Zhang Yifan Lii Zhigang Wu Anton Polishko Huiming Zhang Viswanathan Chinnusamy Stefano Lonardi Jian-Kang Zhu Renyi Liu Hailing Jin 

机构地区：[1]Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA [2]Department of Botany and Plant Sciences and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA [3]Computer Science and Engineering, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA [4]Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA [5]Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India [6]Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China

出　　处：《Molecular Plant》2013年第3期704-715,共12页分子植物（英文版）

摘　　要：ABSTRACT A large proportion of eukaryotic genomes is tranScribed from both positive and negative strands of DNA and thus may generate overlapping sense and antisense transcripts. Some of these so-called natural antisense transcripts （NATs） are possibly co-regulated. When the overlapping sense and antisense transcripts are expressed at the same time in the same cell in response to various developmental and environmental cues; they may form double-stranded RNAs, which could be recognized by the small RNA biogenesis machinery and processed into small interfering RNAs （siRNAs）. cis-NAT-derived siRNAs （nat-siRNAs） are present in plants, animals, and fungi. In plants, the presence of nat-siRNAs is supported not only by Northern blot and genetic analyses, but also by the fact that there is an overall sixfold enrichment of siRNAs in the overlapping regions of cis-NATs and 19%-29% of the siRNA-generating cis-NATs in plants give rise to siRNAs only in their overlapping regions. Silencing mediated by nat-siRNAs is one of the mechanisms for regulating the expression of the cis-NATs. This review focuses on challenging issues related to the biogenesis mechanisms as well as regulation and detection of nat-siRNAs. The advantages and limitations of new technologies for detecting cis-NATs, including direct RNA sequencing and strand-specific RNA sequencing, are also discussed.ABSTRACT A large proportion of eukaryotic genomes is tranScribed from both positive and negative strands of DNA and thus may generate overlapping sense and antisense transcripts. Some of these so-called natural antisense transcripts （NATs） are possibly co-regulated. When the overlapping sense and antisense transcripts are expressed at the same time in the same cell in response to various developmental and environmental cues; they may form double-stranded RNAs, which could be recognized by the small RNA biogenesis machinery and processed into small interfering RNAs （siRNAs）. cis-NAT-derived siRNAs （nat-siRNAs） are present in plants, animals, and fungi. In plants, the presence of nat-siRNAs is supported not only by Northern blot and genetic analyses, but also by the fact that there is an overall sixfold enrichment of siRNAs in the overlapping regions of cis-NATs and 19%-29% of the siRNA-generating cis-NATs in plants give rise to siRNAs only in their overlapping regions. Silencing mediated by nat-siRNAs is one of the mechanisms for regulating the expression of the cis-NATs. This review focuses on challenging issues related to the biogenesis mechanisms as well as regulation and detection of nat-siRNAs. The advantages and limitations of new technologies for detecting cis-NATs, including direct RNA sequencing and strand-specific RNA sequencing, are also discussed.

关 键 词：gene expression gene regulation gene silencing. 

分 类 号：Q959.8[生物学—动物学] S831.1[农业科学—畜牧学]