title: Tracking miRNA precursor metabolic products and processing sites through completely analyzing high-throughput sequencing data.
abstract: The small non-coding important regulatory molecules, microRNAs (miRNAs), have been widely and deeply studied especially combining high-throughput sequencing technologies. Here, we attempted to track detailed miRNA precursor metabolic products and gain further insight into pre-miRNA processing by completely analyzing high-throughput sequencing data. Highly expressed miRNA precursors could be entirely covered by various short RNAs and small RNA fragments with a hierarchical distribution. miRNAs and some miRNA* regions were detected quite abundant short RNAs as expected, while other regions of precursors were found shorter RNAs or small fragments with fewer sequence counts. Furthermore, we developed a method to analyze relative expression levels of special RNA classes according to divergence of 5' and 3' ends, respectively. Generally, there were several quite abundant RNA classes from a given miRNA locus, which suggested dominant cleavage sites of Drosha and Dicer during pre-miRNA processing. Compared with 3' end, dominant cleavage site in 5' end always focused on a specific position, which ensured conservation of the identity of miRNA (5'-seed sequence, nucleotides 2-8). Overall, a comprehensive analysis of sequencing data can be used to track pre-miRNA metabolic products and mechanism of pre-miRNA processing and metabolism.
authors.affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China. gl8008@163.com
authors.forename: Li
authors.initials: L
authors.lastname: Guo
authors.forename: Hailing
authors.initials: H
authors.lastname: Li
authors.forename: Jiafeng
authors.initials: J
authors.lastname: Lu
authors.forename: Qi
authors.initials: Q
authors.lastname: Yang
authors.forename: Qinyu
authors.initials: Q
authors.lastname: Ge
authors.forename: Wanjun
authors.initials: W
authors.lastname: Gu
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Bai
authors.forename: Zuhong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D002681:China; D005260:Female; D020869:Gene Expression Profiling; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism*
chemical_list: D035683:MicroRNAs