title: 3' and 5' microRNA-end post-biogenesis modifications in plant transcriptomes: Evidences from small RNA next generation sequencing data analysis.
abstract: 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.
authors.affiliation: Bioinformatics Laboratory, Structural and Computational Biology Group, ICGEB, New Delhi, India. Electronic address: shradha@icgeb.res.in.
authors.forename: Shradha
authors.initials: S
authors.lastname: Saraf
authors.affiliation: Plant Molecular Biology Group, ICGEB, New Delhi, India. Electronic address: neeti@icgeb.res.in.
authors.forename: Neeti
authors.initials: N
authors.lastname: Sanan-Mishra
authors.affiliation: School of Chemistry and Molecular Biosciences, The University of Queensland, Australia. Electronic address: nial.gursanscky@gmi.oeaw.ac.at.
authors.forename: Nial R
authors.initials: NR
authors.lastname: Gursanscky
authors.affiliation: School of Chemistry and Molecular Biosciences, The University of Queensland, Australia. Electronic address: b.carroll@uq.edu.au.
authors.forename: Bernard J
authors.initials: BJ
authors.lastname: Carroll
authors.affiliation: Bioinformatics Laboratory, Structural and Computational Biology Group, ICGEB, New Delhi, India. Electronic address: dinesh@icgeb.res.in.
authors.forename: Dinesh
authors.initials: D
authors.lastname: Gupta
authors.affiliation: Genetics Department, Univ. of Delhi, South Campus, New Delhi, India. Electronic address: sunilmukherjeeudsc@gmail.com.
authors.forename: Sunil Kumar
authors.initials: SK
authors.lastname: Mukherjee
mesh_terms: D035683:MicroRNAs / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D035683:MicroRNAs
keywords: AGO1; Modifications; Next generation sequencing; RDR6; miRNA