Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues.

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.

[1]  Wu Wei,et al.  RNA Polymerase II Collision Interrupts Convergent Transcription , 2012, Molecular cell.

[2]  Jonathan Schug,et al.  Widespread distribution of antisense transcripts in the Plasmodium falciparum genome. , 2004, Molecular and biochemical parasitology.

[3]  Charles W. Melnyk,et al.  Silencing signals in plants: a long journey for small RNAs , 2011, Genome Biology.

[4]  C. Pikaard,et al.  Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes , 2008, Cell.

[5]  James C. Carrington,et al.  Specialization and evolution of endogenous small RNA pathways , 2007, Nature Reviews Genetics.

[6]  Weixiong Zhang,et al.  Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks , 2010, Plant Molecular Biology.

[7]  Q. Jin,et al.  Profiles of Small Non-Coding RNAs in Schistosoma japonicum during Development , 2011, PLoS neglected tropical diseases.

[8]  Jian Zhang,et al.  PlantNATsDB: a comprehensive database of plant natural antisense transcripts , 2011, Nucleic Acids Res..

[9]  P. Flicek,et al.  Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues , 2009, Nucleic acids research.

[10]  Shivakundan Singh Tej,et al.  Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing , 2004, Nature Biotechnology.

[11]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[12]  K. Kinzler,et al.  The Antisense Transcriptomes of Human Cells , 2008, Science.

[13]  Paul Bertone,et al.  Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. , 2010, RNA.

[14]  Hailing Jin,et al.  Role of small RNAs in host-microbe interactions. , 2010, Annual review of phytopathology.

[15]  D. Bartel,et al.  MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.

[16]  A. Werner,et al.  Processing of naturally occurring sense/antisense transcripts of the vertebrate Slc34a gene into short RNAs. , 2008, Physiological genomics.

[17]  Joseph R. Ecker,et al.  Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome , 2007, Cell.

[18]  C. Pikaard,et al.  Roles of RNA polymerase IV in gene silencing. , 2008, Trends in plant science.

[19]  Jeffrey P. Mower,et al.  RNAi in Budding Yeast , 2009, Science.

[20]  S. Ding.  RNA-based antiviral immunity , 2010, Nature Reviews Immunology.

[21]  S. Sunkin,et al.  Specific expression of long noncoding RNAs in the mouse brain , 2008, Proceedings of the National Academy of Sciences.

[22]  D. Baulcombe,et al.  Systemic Spread of Sequence-Specific Transgene RNA Degradation in Plants Is Initiated by Localized Introduction of Ectopic Promoterless DNA , 1998, Cell.

[23]  Oliver H. Tam,et al.  Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes , 2008, Nature.

[24]  Mily Ron,et al.  Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis. , 2010, Genes & development.

[25]  Ping Wu,et al.  Small RNAs in angiosperms: sequence characteristics, distribution and generation , 2010, Bioinform..

[26]  Tamas Dalmay,et al.  An RNA-Dependent RNA Polymerase Gene in Arabidopsis Is Required for Posttranscriptional Gene Silencing Mediated by a Transgene but Not by a Virus , 2000, Cell.

[27]  F. Rosenbauer,et al.  PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element. , 2008, Genes & development.

[28]  D. Higgs,et al.  Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease , 2003, Nature Genetics.

[29]  Charles W. Melnyk,et al.  Intercellular and systemic movement of RNA silencing signals , 2011, The EMBO journal.

[30]  A. Werner,et al.  What do natural antisense transcripts regulate? , 2009, RNA biology.

[31]  Z. Weng,et al.  Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells , 2008, Science.

[32]  Yongfeng Jin,et al.  Nontemplated nucleotide addition prior to polyadenylation: a comparison of Arabidopsis cDNA and genomic sequences. , 2004, RNA.

[33]  O. Voinnet,et al.  Roles of plant small RNAs in biotic stress responses. , 2009, Annual review of plant biology.

[34]  Masaru Tomita,et al.  Comparative expression analysis uncovers novel features of endogenous antisense transcription. , 2008, Human molecular genetics.

[35]  Shang Gao,et al.  Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function , 2012, Genome Biology.

[36]  A. Werner,et al.  Expression profiling of antisense transcripts on DNA arrays. , 2007, Physiological genomics.

[37]  G. Barton,et al.  Direct Sequencing of Arabidopsis thaliana RNA Reveals Patterns of Cleavage and Polyadenylation , 2012, Nature Structural &Molecular Biology.

[38]  Krystyna A. Kelly,et al.  Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis , 2009, Nature.

[39]  H. Vaucheret,et al.  Form, Function, and Regulation of ARGONAUTE Proteins , 2010, Plant Cell.

[40]  N. Perrimon,et al.  An endogenous small interfering RNA pathway in Drosophila , 2008, Nature.

[41]  Y. Sakaki,et al.  Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes , 2008, Nature.

[42]  Joseph M. Dale,et al.  Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome , 2003, Science.

[43]  Vladimir Vacic,et al.  Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis , 2008, BMC Molecular Biology.

[44]  E. Cuppen,et al.  Limitations and possibilities of small RNA digital gene expression profiling , 2009, Nature Methods.

[45]  G. Phillips,et al.  Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[46]  B. Roe,et al.  Cloning, characterization and expression analysis of porcine microRNAs , 2009, BMC Genomics.

[47]  N. Proudfoot,et al.  Transcriptional collision between convergent genes in budding yeast , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[48]  Sylvain Foissac,et al.  New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism , 2010, Nature.

[49]  Hailing Jin.  Endogenous small RNAs and antibacterial immunity in plants , 2008, FEBS letters.

[50]  Xiu-Jie Wang,et al.  Identification and Characterization of Small RNAs in the Hyperthermophilic Archaeon Sulfolobus solfataricus , 2012, PloS one.

[51]  Miao Sun,et al.  Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. , 2006, Genome research.

[52]  C. Wahlestedt,et al.  Regulatory roles of natural antisense transcripts , 2009, Nature Reviews Molecular Cell Biology.

[53]  Madhur Kumar,et al.  Nuclear antisense RNA induces extensive adenosine modifications and nuclear retention of target transcripts. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[55]  S. Luo,et al.  RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. , 2011, RNA.

[56]  C. Rivetti,et al.  Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy , 2006, Nucleic acids research.

[57]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[58]  L. Hurst,et al.  Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts. , 2005, Trends in genetics : TIG.

[59]  Ying Liu,et al.  R2D2 Organizes Small Regulatory RNA Pathways in Drosophila , 2010, Molecular and Cellular Biology.

[60]  Michael Q. Zhang,et al.  Regulating Gene Expression through RNA Nuclear Retention , 2005, Cell.

[61]  H. Vaucheret,et al.  Functions of microRNAs and related small RNAs in plants , 2006, Nature Genetics.

[62]  C. Milcarek,et al.  Expression of the thyroid hormone receptor gene, erbAalpha, in B lymphocytes: alternative mRNA processing is independent of differentiation but correlates with antisense RNA levels. , 1997, Nucleic acids research.

[63]  O. Borsani,et al.  Endogenous siRNAs Derived from a Pair of Natural cis-Antisense Transcripts Regulate Salt Tolerance in Arabidopsis , 2005, Cell.

[64]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.

[65]  M. Marra,et al.  Extensive relationship between antisense transcription and alternative splicing in the human genome. , 2011, Genome research.

[66]  E. Zubko,et al.  A natural antisense transcript of the Petunia hybrida Sho gene suggests a role for an antisense mechanism in cytokinin regulation , 2007, The Plant journal : for cell and molecular biology.

[67]  Hailing Jin,et al.  A pathogen-inducible endogenous siRNA in plant immunity , 2006, Proceedings of the National Academy of Sciences.

[68]  Hailing Jin,et al.  Host small RNAs are big contributors to plant innate immunity. , 2009, Current opinion in plant biology.

[69]  Guoli Ji,et al.  Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation , 2011, Proceedings of the National Academy of Sciences.

[70]  Neil R Smalheiser,et al.  Endogenous siRNAs and noncoding RNA-derived small RNAs are expressed in adult mouse hippocampus and are up-regulated in olfactory discrimination training. , 2011, RNA.

[71]  X. Shirley Liu,et al.  Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species , 2006, Nucleic acids research.

[72]  K. Nieselt,et al.  Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes , 2005, Nucleic acids research.

[73]  Ying Lu,et al.  Strand-specific RNA-seq reveals widespread occurrence of novel cis- natural antisense transcripts in rice , 2012, BMC Genomics.

[74]  Yitzhak Pilpel,et al.  Genome‐wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms , 2006, EMBO reports.

[75]  Ramanjulu Sunkar,et al.  Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. , 2008, Genome research.

[76]  Matthew D. Schultz,et al.  Surveillance of 3′ Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis , 2012, G3: Genes | Genomes | Genetics.

[77]  A. Sandelin,et al.  Hidden layers of human small RNAs , 2008, BMC Genomics.

[78]  Terry Gaasterland,et al.  Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana , 2005, Genome Biology.