Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

BackgroundPollen development in flowering plants requires strict control of the gene expression program and genetic information stability by mechanisms possibly including the miRNA pathway. However, our understanding of the miRNA pathway in pollen development remains limited, and the dynamic profile of miRNAs in developing pollen is unknown.ResultsUsing next-generation sequencing technology, we pyrosequenced small RNA populations from rice uninucleate microspores to tricellular pollen and control sporophytic tissues at the genome-wide level. We identified 292 known miRNAs, including members of all 20 families conserved in plants, and 75 novel miRNAs. Of the 292 known miRNAs, 202 were expressed, with 103 enriched, in developing pollen. More than half of these novel miRNAs displayed pollen-or stage-specific expression. Furthermore, analyzing the 367 miRNAs and their predicted targets indicated that correlation in expression profiles of pollen-enriched known miRNAs and their targets significantly differs from that of sporophyte-enriched known miRNAs and their targets in some functional terms, while novel miRNAs appeared to negatively regulate their targets. Importantly, gene ontology abundance analysis demonstrated chromatin assembly and disassembly was important in the targets of bicellular pollen-expressed novel miRNAs. Principal component analysis revealed pollen of all three stages was discriminated from sporophytes, largely because of the novel and non-conserved known miRNAs.ConclusionsOur study, for the first time, revealed the differences in composition and expression profiles of miRNAs between developing pollen and sporophytes, with novel and non-conserved known miRNAs the main contributors. Our results suggest the important roles of the miRNA pathway in pollen development.

[1]  D. Marks,et al.  The small RNA profile during Drosophila melanogaster development. , 2003, Developmental cell.

[2]  Ramanjulu Sunkar,et al.  Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. , 2009, RNA.

[3]  Y. Hiei,et al.  Map-based cloning of a fertility restorer gene, Rf-1, in rice (Oryza sativa L.). , 2004, The Plant journal : for cell and molecular biology.

[4]  E. F. Walton,et al.  Plant Methods Protocol: a Highly Sensitive Rt-pcr Method for Detection and Quantification of Micrornas , 2022 .

[5]  C. Robin Buell,et al.  The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants , 2004, Nucleic Acids Res..

[6]  Olivier Voinnet,et al.  Two classes of short interfering RNA in RNA silencing , 2002, The EMBO journal.

[7]  Sean R. Eddy,et al.  Rfam: annotating non-coding RNAs in complete genomes , 2004, Nucleic Acids Res..

[8]  Huiling Xue,et al.  MicroRNA miR-24 inhibits erythropoiesis by targeting activin type I receptor ALK4. , 2008, Blood.

[9]  Michael Borg,et al.  Male gametophyte development: a molecular perspective. , 2009, Journal of experimental botany.

[10]  Zhiwei Cheng,et al.  Gibberellin Acts through Jasmonate to Control the Expression of MYB21, MYB24, and MYB57 to Promote Stamen Filament Growth in Arabidopsis , 2009, PLoS genetics.

[11]  David Twell,et al.  Transcriptome analysis of haploid male gametophyte development in Arabidopsis , 2004, Genome Biology.

[12]  Ruiqiang Li,et al.  SOAP: short oligonucleotide alignment program , 2008, Bioinform..

[13]  D. Zilberman,et al.  Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation , 2010, Science.

[14]  Y. Qi,et al.  Rice MicroRNA Effector Complexes and Targets[C][W] , 2009, The Plant Cell Online.

[15]  N. Chua,et al.  MicroRNA Directs mRNA Cleavage of the Transcription Factor NAC1 to Downregulate Auxin Signals for Arabidopsis Lateral Root Development , 2005, The Plant Cell Online.

[16]  C. Mariani,et al.  Ethylene response to pollen tube growth in Nicotiana tabacum flowers , 2002, Planta.

[17]  Wenying Xu,et al.  Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa , 2010, BMC Genomics.

[18]  Huanming Yang,et al.  Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. , 2010, Genome research.

[19]  J. Reed,et al.  Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction , 2006, Development.

[20]  G. Le Trionnaire,et al.  Small RNAs in angiosperm gametophytes: from epigenetics to gamete development. , 2010, Genes & development.

[21]  X. Liu,et al.  Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize[W] , 2009, The Plant Cell Online.

[22]  Elliot M Meyerowitz,et al.  Redundancy and specialization among plant microRNAs: role of the MIR164 family in developmental robustness , 2007, Development.

[23]  Hui Zhou,et al.  starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data , 2010, Nucleic Acids Res..

[24]  Jörg D. Becker,et al.  Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen , 2009, Cell.

[25]  H. Sano,et al.  Methylated DNA-Binding Proteins from Arabidopsis1 , 2003, Plant Physiology.

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

[27]  Shihshieh Huang,et al.  Transgenic Studies on the Involvement of Cytokinin and Gibberellin in Male Development , 2003, Plant Physiology.

[28]  D. Bartel,et al.  Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. , 2004, Molecular cell.

[29]  B. Shuai,et al.  Profiling microRNA expression in Arabidopsis pollen using microRNA array and real-time PCR , 2009, BMC Plant Biology.

[30]  F. Tang.  Small RNAs in mammalian germline: Tiny for immortal. , 2010, Differentiation; research in biological diversity.

[31]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[32]  Yuichiro Watanabe,et al.  Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[34]  Ho Bang Kim,et al.  A knock-out mutation in allene oxide synthase results in male sterility and defective wound signal transduction in Arabidopsis due to a block in jasmonic acid biosynthesis. , 2002, The Plant journal : for cell and molecular biology.

[35]  J. Feijó,et al.  Gene Family Analysis of the Arabidopsis Pollen Transcriptome Reveals Biological Implications for Cell Growth, Division Control, and Gene Expression Regulation1[w] , 2005, Plant Physiology.

[36]  C. Caron,et al.  Establishment of male-specific epigenetic information. , 2005, Gene.

[37]  Sam Griffiths-Jones,et al.  The microRNA Registry , 2004, Nucleic Acids Res..

[38]  J. Trasler.  Epigenetics in spermatogenesis , 2009, Molecular and Cellular Endocrinology.

[39]  D. Zilberman,et al.  RNA Silencing Genes Control de Novo DNA Methylation , 2004, Science.

[40]  J. Feijó,et al.  Comparative Transcriptomics of Arabidopsis Sperm Cells1[C][W] , 2008, Plant Physiology.

[41]  I. Henderson,et al.  Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning , 2006, Nature Genetics.

[42]  G. Falasca,et al.  Auxin Regulates Arabidopsis Anther Dehiscence, Pollen Maturation, and Filament Elongation[W] , 2008, The Plant Cell Online.

[43]  Ryan D. Morin,et al.  Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. , 2008, Genome research.

[44]  Yuanji Zhang,et al.  miRU: an automated plant miRNA target prediction server , 2005, Nucleic Acids Res..

[45]  Ian Small,et al.  On the expansion of the pentatricopeptide repeat gene family in plants. , 2008, Molecular biology and evolution.

[46]  R. Grant-Downton,et al.  Small RNA pathways are present and functional in the angiosperm male gametophyte. , 2009, Molecular plant.

[47]  R. Schmid,et al.  MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana , 2009, BMC Genomics.

[48]  B. Reinhart,et al.  MicroRNAs in plants. , 2002, Genes & development.

[49]  Xuemei Chen,et al.  Small RNAs and their roles in plant development. , 2009, Annual review of cell and developmental biology.

[50]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[51]  Baohong Zhang,et al.  Conservation and divergence of plant microRNA genes. , 2006, The Plant journal : for cell and molecular biology.

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

[53]  L. Graham,et al.  The origin of alternation of generations in land plants: a focus on matrotrophy and hexose transport. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[54]  O. Voinnet.  Origin, Biogenesis, and Activity of Plant MicroRNAs , 2009, Cell.

[55]  F. Gubler,et al.  The Arabidopsis GAMYB-Like Genes, MYB33 and MYB65, Are MicroRNA-Regulated Genes That Redundantly Facilitate Anther Development , 2005, The Plant Cell Online.

[56]  Xiaofeng Cao,et al.  ARGONAUTE4 Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation , 2003, Science.

[57]  D. Bartel,et al.  Criteria for Annotation of Plant MicroRNAs , 2008, The Plant Cell Online.

[58]  F. S. Bao,et al.  Small RNA Deep Sequencing Reveals Role for Arabidopsis thaliana RNA-Dependent RNA Polymerases in Viral siRNA Biogenesis , 2009, PloS one.

[59]  Yun Zheng,et al.  Identification of novel and candidate miRNAs in rice by high throughput sequencing , 2008, BMC Plant Biology.

[60]  Jian Yu,et al.  Male mice defective in the DNA mismatch repair gene PMS2 exhibit abnormal chromosome synapsis in meiosis , 1995, Cell.

[61]  Yan Li,et al.  Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post‐embryogenic development , 2006, FEBS letters.

[62]  Zhonghuai Xiang,et al.  MicroRNAs of Bombyx mori identified by Solexa sequencing , 2010, BMC Genomics.

[63]  V. Moulton,et al.  Deciphering the diversity of small RNAs in plants: the long and short of it. , 2009, Briefings in functional genomics & proteomics.

[64]  K. Livak,et al.  Real-time quantification of microRNAs by stem–loop RT–PCR , 2005, Nucleic acids research.

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

[66]  S. Luo,et al.  Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends , 2008, Nature Biotechnology.

[67]  Yun Zheng,et al.  Transcriptome-wide identification of microRNA targets in rice. , 2010, The Plant journal : for cell and molecular biology.

[68]  D. Bartel,et al.  A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. , 2006, Genes & development.

[69]  G. Hannon,et al.  Conserved themes in small-RNA-mediated transposon control. , 2008, Trends in cell biology.

[70]  J. Zhai,et al.  Conservation and divergence in eukaryotic DNA methylation , 2010, Proceedings of the National Academy of Sciences.

[71]  Jason S. Cumbie,et al.  High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes , 2007, PloS one.

[72]  Robert D. Finn,et al.  Rfam: updates to the RNA families database , 2008, Nucleic Acids Res..

[73]  Bin Liu,et al.  Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs) , 2008, Proceedings of the National Academy of Sciences.

[74]  Olivier Panaud,et al.  Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice , 2008, BMC Plant Biology.

[75]  R. Zhao,et al.  Knockdown of Dicer in MCF-7 human breast carcinoma cells results in G1 arrest and increased sensitivity to cisplatin. , 2009, Oncology reports.

[76]  S. Kauppinen,et al.  Spatio-temporal accumulation of microRNAs is highly coordinated in developing plant tissues. , 2006, The Plant journal : for cell and molecular biology.

[77]  T. Kakutani,et al.  Heritable epigenetic mutation of a transposon‐flanked Arabidopsis gene due to lack of the chromatin‐remodeling factor DDM1 , 2007, The EMBO journal.

[78]  Yijun Qi,et al.  DNA methylation mediated by a microRNA pathway. , 2010, Molecular cell.

[79]  K. Shinozaki,et al.  The Arabidopsis SDG4 contributes to the regulation of pollen tube growth by methylation of histone H3 lysines 4 and 36 in mature pollen. , 2008, Developmental biology.

[80]  Stijn van Dongen,et al.  miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..

[81]  Assaf Zemach,et al.  Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. , 2003, The Plant journal : for cell and molecular biology.

[82]  Zachary Pincus,et al.  Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development , 2009, Genome Biology.

[83]  Baohong Zhang,et al.  Identification of 188 conserved maize microRNAs and their targets , 2006, FEBS letters.

[84]  D. Bartel,et al.  Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome , 2008, Current Biology.

[85]  Patrick Achard,et al.  Modulation of floral development by a gibberellin-regulated microRNA , 2004, Development.