Identification of potential microRNAs and their ta

Authors: Vignesh Dhandapani Nirala Ramchiary Parameswari Paul Joonki Kim Sun Hee Choi Jeongyeo Lee Yoonkang Hur Yong Pyo Lim

Publish Date: 2011/06/03

Volume: 32, Issue: 1, Pages: 21-37

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Abstract

MicroRNAs miRNAs are recently discovered noncoding small regulatory RNA molecules that negatively regulate gene expression Although many miRNAs are identified and validated in many plant species they remain largely unknown in Brassica rapa AA 2n = 20 B rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables oilseeds and fodder crop production In this study we identified 186 miRNAs belonging to 55 families in B rapa by using comparative genomics The lengths of identified mature and premiRNAs ranged from 18 to 22 and 66 to 305 nucleotides respectively Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B rapa miRNA suggesting that it plays an important role in miRNAmediated gene regulation Overall adenine and guanine were predominant in mature miRNAs while adenine and uracil were predominant in premiRNA sequences One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family which differs by 1 nucleotide at the 20th position was identified In silico analyses using previously established methods predicted 66 miRNA target mRNAs for 33 miRNA families The majority of the target genes were transcription factors that regulate plant growth and development followed by a few target genes that are involved in fatty acid metabolism glycolysis biotic and abiotic stresses and other cellular processes Northern blot and qRTPCR analyses of RNA samples prepared from different B rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B rapa

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