3' and 5' microRNA-end post-biogenesis modifications in plant transcriptomes: Evidences from small RNA next generation sequencing data analysis.

The processing of miRNA from its precursors is a precisely regulated process and after biogenesis, the miRNAs are amenable to different kinds of modifications by the addition or deletion of nucleotides at the terminal ends. However, the mechanism and functions of such modifications are not well studied in plants. In this study, we have specifically analysed the terminal end non-templated miRNA modifications, using NGS data of rice, tomato and Arabidopsis small RNA transcriptomes from different tissues and physiological conditions. Our analysis reveals template independent terminal end modifications in the mature as well as passenger strands of the miRNA duplex. Interestingly, it is also observed that miRNA sequences terminating with a cytosine (C) at the 3' end undergo a higher percentage of 5' end modifications. The terminal end modifications did not correlate with the miRNA abundances and are independent of tissue types, physiological conditions and plant species. Our analysis indicates that the addition of nucleotides at miRNA ends is not influenced by the absence of RNA dependent RNA polymerase 6. Moreover the terminal end modified miRNAs are also observed amongst AGO1 bound small RNAs and have potential to alter target, indicating its important functional role in repression of gene expression.

[1]  Ammar S Naqvi,et al.  Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. , 2011, Genome research.

[2]  Shougong Zhang,et al.  A genome-wide survey of microRNA truncation and 3′ nucleotide addition events in larch (Larix leptolepis) , 2012, Planta.

[3]  Gregory J. Hannon,et al.  Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide , 2008, Cell.

[4]  Lei Li,et al.  miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants , 2011, Bioinform..

[5]  C. Nusbaum,et al.  Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. , 2010, Genes & development.

[6]  V. Kim,et al.  Modifications of Small RNAs and Their Associated Proteins , 2010, Cell.

[7]  Herbert H. Tsang,et al.  Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications , 2009, Nucleic acids research.

[8]  Xuemei Chen,et al.  microRNA biogenesis and function in plants , 2005, FEBS letters.

[9]  William J. Cody,et al.  Algorithm 715: SPECFUN–a portable FORTRAN package of special function routines and test drivers , 1993, TOMS.

[10]  Y. Hayashizaki,et al.  A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. , 2010, Genome research.

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

[12]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[13]  V. Chiang,et al.  Adenylation of plant miRNAs , 2009, Nucleic acids research.

[14]  Xuemei Chen,et al.  Biochemical Activities of Arabidopsis RNA-dependent RNA Polymerase 6* , 2008, Journal of Biological Chemistry.

[15]  Xuemei Chen,et al.  Methylation Protects miRNAs and siRNAs from a 3′-End Uridylation Activity in Arabidopsis , 2005, Current Biology.

[16]  C. Langford,et al.  5′ isomiR variation is of functional and evolutionary importance , 2014, Nucleic acids research.

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

[18]  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.

[19]  Ryan D. Morin,et al.  Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. , 2008, Genome research.

[20]  Stefan L Ameres,et al.  Diversifying microRNA sequence and function , 2013, Nature Reviews Molecular Cell Biology.

[21]  Dinesh Gupta,et al.  miRMOD: a tool for identification and analysis of 5′ and 3′ miRNA modifications in Next Generation Sequencing small RNA data , 2015, PeerJ.

[22]  Li Guo,et al.  A Comprehensive Survey of miRNA Repertoire and 3′ Addition Events in the Placentas of Patients with Pre-Eclampsia from High-Throughput Sequencing , 2011, PloS one.

[23]  S. Mukherjee,et al.  Transgenic tomato plants expressing artificial microRNAs for silencing the pre-coat and coat proteins of a begomovirus, Tomato leaf curl New Delhi virus, show tolerance to virus infection. , 2013, Virus research.

[24]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[25]  Athanasios Fevgas,et al.  DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions , 2014, Nucleic Acids Res..