title: Genome-wide identification and functional annotation of miRNAs in anti-inflammatory plant and their cross-kingdom regulation in Homo sapiens.
abstract: MicroRNAs (miRNAs) are newly discovered non-coding small (~17-24 nucleotide) RNAs that regulate gene expression of its target mRNA at the post-transcriptional levels. In this study, total 12,593 ESTs of Curcuma longa were taken from database of expressed sequence tags (dbEST) and clustered into 2821 contigs using EGassembler web server. Precursor miRNAs (pre-miRNAs) were predicted from these contigs that folded into stem-loop structure using MFold server. Thirty-four mature C. longa miRNAs (clo-miRNAs) were identified from pre-miRNAs having targets involved in various important functions of plant such as self-defence, growth and development, alkaloid metabolic pathway and ethylene signalling process. Sequence analysis of identified clo-miRNAs indicated that 56% miRNAs belong to ORF and 44% belong to non-ORF region. clo-mir-5 and clo-mir-6 were established as the conserved miRNAs, whereas clo-mir-20 was predicted to be the most stable miRNA. Phylogenetic analysis carried out by molecular evolutionary genetics analysis (MEGA) software indicated close evolutionary relationship of clo-mir-5075 with osa-MIR5075. Further, identified clo-miRNAs were checked for their cross-kingdom regulatory potential. clo-mir-14 was found to regulate various gene transcripts in humans that has been further investigated for its biostability in foetal bovine serum (FBS). The results indicated higher degree of stability of clo-mir-14 (48 h) in FBS. Thus, contribution of this miRNA to the cellular immune response during the inflamed condition of rheumatoid arthritis and adequate stability may make it a good choice for the therapeutic agent in near future.
authors.affiliation: a Department of Genomics and Molecular Medicine , Institute of Genomics and Integrative Biology , Delhi , India.
authors.forename: Ankita
authors.initials: A
authors.lastname: Sharma
authors.affiliation: b School of Biotechnology , Shobhit University , Meerut , Uttar Pradesh , India.
authors.forename: Sarika
authors.initials: S
authors.lastname: Sahu
authors.affiliation: a Department of Genomics and Molecular Medicine , Institute of Genomics and Integrative Biology , Delhi , India.
authors.forename: Pooja
authors.initials: P
authors.lastname: Kumari
authors.affiliation: a Department of Genomics and Molecular Medicine , Institute of Genomics and Integrative Biology , Delhi , India.
authors.forename: Soundhara Rajan
authors.initials: SR
authors.lastname: Gopi
authors.affiliation: c Department of Orthopaedics , All India Institute of Medical Science , New Delhi , India.
authors.forename: Rajesh
authors.initials: R
authors.lastname: Malhotra
authors.affiliation: a Department of Genomics and Molecular Medicine , Institute of Genomics and Integrative Biology , Delhi , India.
authors.forename: Sagarika
authors.initials: S
authors.lastname: Biswas
mesh_terms: D001172:Arthritis, Rheumatoid / Q000097:blood / Q000235:genetics* / Q000473:pathology; D020029:Base Pairing; D001483:Base Sequence; D030024:Curcuma / Q000737:chemistry*; D020224:Expressed Sequence Tags; D016326:Extracellular Matrix Proteins / Q000097:blood* / Q000235:genetics; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D006801:Humans; D035683:MicroRNAs / Q000097:blood* / Q000235:genetics / Q000302:isolation & purification; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D010936:Plant Extracts / Q000737:chemistry*; D011509:Proteoglycans / Q000097:blood / Q000235:genetics; D020871:RNA Stability; D018749:RNA, Plant / Q000097:blood* / Q000235:genetics / Q000302:isolation & purification; D043562:Receptors, G-Protein-Coupled / Q000097:blood* / Q000235:genetics; D016415:Sequence Alignment; D013816:Thermodynamics
chemical_list: D016326:Extracellular Matrix Proteins; D035683:MicroRNAs; D010936:Plant Extracts; D011509:Proteoglycans; D018749:RNA, Plant; D043562:Receptors, G-Protein-Coupled; C012596:turmeric extract
keywords: Curcuma longa; Micro-RNA; contigs; cross-kingdom regulation; expressed sequence tags; rheumatoid arthritis