title: Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues.
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.
authors.affiliation: Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Zhang
authors.forename: Yifan
authors.initials: Y
authors.lastname: Lii
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Wu
authors.forename: Anton
authors.initials: A
authors.lastname: Polishko
authors.forename: Huiming
authors.initials: H
authors.lastname: Zhang
authors.forename: Viswanathan
authors.initials: V
authors.lastname: Chinnusamy
authors.forename: Stefano
authors.initials: S
authors.lastname: Lonardi
authors.forename: Jian-Kang
authors.initials: JK
authors.lastname: Zhu
authors.forename: Renyi
authors.initials: R
authors.lastname: Liu
authors.forename: Hailing
authors.initials: H
authors.lastname: Jin
mesh_terms: D000818:Animals; D004777:Environment; D056890:Eukaryota / Q000378:metabolism; D005658:Fungi / Q000378:metabolism; D063245:Plant Development; D016372:RNA, Antisense / Q000378:metabolism*; D018749:RNA, Plant / Q000378:metabolism*
chemical_list: D016372:RNA, Antisense; D018749:RNA, Plant
keywords: gene expression; gene regulation; gene silencing.