Landscape of RNAs in human lumbar disc degeneration

// Ping-Heng Lan 1, 11, * , Zhi-Heng Liu 2, * , Yan-Jun Pei 1 , Zhi-Gang Wu 3, 4 , Yang Yu 5, 6 , Yong-Feng Yang 7 , Xu Liu 8 , Lu Che 8 , Chi-Jiao Ma 9 , Yan-Ke Xie 8 , Qing-Jie Hu 8 , Zhong-Yuan Wan 10 , Hai-Qiang Wang 1 1 Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University, Xi’an, P. R. China 2 Department of Orthopaedics, Xi’an Air Force Hospital, Xi’an, P.R. China 3 The Second Department of Surgery, No. 518 Hospital of the PLA, Xi’an, P. R. China 4 Department of Orthopaedic Surgery, Lanzhou General Hospital of Lanzhou Military Region, PLA, Lanzhou, P. R. China 5 State Key Laboratory of Military Stomatology, Department of Periodontology, School of Stomatology, Fourth Military Medical University, Xi’an, P. R. China 6 Shaanxi Key Laboratory of Stomatology, Biomaterials Unit, School of Stomatology, Fourth Military Medical University, Xi’an, P. R. China 7 Company Eleven, Brigade of Undergraduates, Fourth Military Medical University, Xi’an, P. R. China 8 Aerospace Medical School, Fourth Military Medical University, Xi’an, P. R. China 9 The First Hospital of Hanbin Area, Ankang, P. R. China 10 Department of Orthopedics, General Hospital of Beijing Military Command, Beijing, P. R. China 11 Department of Orthopaedics, No. 5 Hospital of the PLA, Yinchuan, P. R. China * These authors contributed equally to this work Correspondence to: Hai-Qiang Wang, email: hqwang@fmmu.edu.cn , drwanghq@163.com Keywords: noncoding RNAs, miRNAs, circRNAs, gene regulation, RNA transcription Received: March 30, 2016      Accepted: August 12, 2016      Published: August 17, 2016 ABSTRACT Accumulating evidence indicates noncoding RNAs (ncRNAs) fine-tune gene expression with mysterious machinery. We conducted a combination of mRNA, miRNA, circRNA, LncRNA microarray analyses on 10 adults’ lumbar discs. Moreover, we performed additional global exploration on RNA interacting machinery in terms of in silico computational pipeline. Here we show the landscape of RNAs in human lumbar discs. In general, the RNA-abundant landscape comprises 14,635 mRNAs (37.93%), 2,059 miRNAs (5.34%), 18,995 LncRNAs (49.23%) and 2,894 (7.5%) circRNAs. Chromosome 1 contributes for RNA transcription at most (10%). Bi-directional transcription contributes evenly for RNA biogenesis, in terms of 5’ to 3’ and 3’ to 5’. Despite the majority of circRNAs are exonic, antisense (1.49%), intergenic (0.035%), intragenic (1.69%), and intronic (6.29%) circRNAs should not be ignored. A single miRNA could interact with a multitude of circRNAs. Notably, CDR1as or ciRS-7 harbors 66 consecutive binding sites for miR-7-5p (previous miR-7), evidencing our pipeline. The majority of binding sites are perfect-matched (78.95%). Collectively, global landscape of RNAs sheds novel insights on RNA interacting mechanisms in human intervertebral disc degeneration.