title: MicroRNAs of rat articular cartilage at different developmental stages identified by Solexa sequencing.
abstract: BACKGROUND
  Expression profiles of microRNAs (miRNAs) can shape the repertoire of proteins expressed in development, differentiation and diseases. This study aimed to identify miRNA profile of articular cartilage at different developmental stages in rats.
  
  
  METHODS
  Three small RNA libraries were constructed from the femoral head cartilage of Sprague-Dawley (SD) rats at postnatal day 0, day 21 and day 42 and sequenced by a deep sequencing approach. Then a bioinformatics approach was employed to distinguish genuine miRNAs from small RNAs represented in the mass sequencing data. The expression of indicated miRNAs was determined by stem-loop RT-qPCR to valuate the consistency with Solexa sequencing.
  
  
  RESULTS
  Two hundred and fifty-eight of 310 known miRNA and miRNA* genes were organized into 91 compact clusters. Two hundred and forty-six miRNAs were detected in all three small RNA libraries of rat articular cartilage. Forty-six, fifty-two and fifty-six miRNA* genes were identified from three small RNA libraries, respectively, and 86 novel miRNA candidate genes were found simultaneously. In addition, 23 known miRNAs were up-regulated (fold change ≥ 4); six were down-regulated (fold change ≤ -4) during articular cartilage development. The predicted targets of differentially expressed miRNAs were locally secreted factors and transcription factors that regulate proliferation and differentiation of chondrocytes. The same expression tendency of indicated miRNAs during articular cartilage development stages was observed by using Solexa sequencing and stem-loop RT-qPCR.
  
  
  CONCLUSIONS
  Our study provided a unique opportunity to decipher how the elaboration of the miRNA repertoire contributes to the development process of articular cartilage.
authors.affiliation: Department of Genetics and Molecular Biology, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, PR China.
authors.forename: J
authors.initials: J
authors.lastname: Sun
authors.forename: N
authors.initials: N
authors.lastname: Zhong
authors.forename: Q
authors.initials: Q
authors.lastname: Li
authors.forename: Z
authors.initials: Z
authors.lastname: Min
authors.forename: W
authors.initials: W
authors.lastname: Zhao
authors.forename: Q
authors.initials: Q
authors.lastname: Sun
authors.forename: L
authors.initials: L
authors.lastname: Tian
authors.forename: H
authors.initials: H
authors.lastname: Yu
authors.forename: Q
authors.initials: Q
authors.lastname: Shi
authors.forename: F
authors.initials: F
authors.lastname: Zhang
authors.forename: S
authors.initials: S
authors.lastname: Lu
mesh_terms: D000375:Aging / Q000235:genetics; D000818:Animals; D002358:Cartilage, Articular / Q000378:metabolism*; D019295:Computational Biology; D004195:Disease Models, Animal; D005269:Femur / Q000737:chemistry*; D020869:Gene Expression Profiling; D006614:Hindlimb / Q000737:chemistry*; D055029:Inverted Repeat Sequences; D035683:MicroRNAs / Q000032:analysis / Q000235:genetics*; D051381:Rats; D017207:Rats, Sprague-Dawley; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D015854:Up-Regulation
chemical_list: D035683:MicroRNAs