title: Exploring the stability of long intergenic non-coding RNA in K562 cells by comparative studies of RNA-Seq datasets.
abstract: BACKGROUND
  The stability of long intergenic non-coding RNAs (lincRNAs) that possess tissue/cell-specific expression, might be closely related to their physiological functions. However, the mechanism associated with stability of lincRNA remains elusive. In this study, we try to study the stability of lincRNA in K562 cells, an important model cell, through comparing two K562 transcriptomes which are obtained from ENCODE Consortium and our sequenced RNA-Seq dataset (PH) respectively.
  
  
  RESULTS
  By lincRNAs analysis pipeline, 1804 high-confidence lincRNAs involving 1564 annotated lincRNAs and 240 putative novel lincRNAs were identified in PH, and 1587 high-confidence lincRNAs including 1429 annotated lincRNAs and 158 putative novel lincRNAs in ENCODE. There are 1009 unique lincRNAs in PH, 792 unique lincRNAs were in ENCODE, and 795 overlapping lincRNAs in both datasets. The analysis of differences in minimum free energy distribution and lincRNA half-life showed that a large proportion of overlapping lincRNAs were more stable than the unique lincRNAs. Most lincRNAs were more unstable than protein-coding RNAs through comparing their minimum free energy.
  
  
  CONCLUSIONS
  Identification of overlapping and unique lincRNAs can be helpful to classify the stability of lincRNAs. Our results suggest that overlapping lincRNAs (relatively stable linRNAs) and unique lincRNAs (relatively unstable lincRNAs) might be involved in different cellular processes.
  
  
  METHODS
  This article has been reviewed by Prof. Oliviero Carugo, Dr. Alistair Forrest and Prof. Manju Bansal.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.forename: Dequan
authors.initials: D
authors.lastname: Zhou
authors.forename: Jing
authors.initials: J
authors.lastname: Tu
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Sipailou #2, Nanjing, Jiangsu Province 210096, China. zhlu@seu.edu.cn.
authors.forename: Zuhong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D030561:Databases, Nucleic Acid; D066264:Datasets as Topic; D015894:Genome, Human / Q000235:genetics; D006207:Half-Life; D006801:Humans; D020014:K562 Cells; D016366:Open Reading Frames / Q000235:genetics; D020871:RNA Stability / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013816:Thermodynamics
chemical_list: D062085:RNA, Long Noncoding