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LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes

  • Xiaowei Chen
  • Yajing Hao
  • Ya Cui
  • Zhen Fan
  • Runsheng ChenEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1870)

Abstract

Long noncoding RNAs (lncRNAs) are pervasively transcribed in various species and play important roles in many biological processes. The biological functions of most lncRNAs remain to be explored. Previous studies have revealed that a large amount of disease-associated variations are located in the lncRNA gene regions. To evaluate the effects of genetic variations on lncRNAs, we constructed a database of genetic variations associated with long noncoding genes, LncVar. In this chapter, we describe the process of collecting data (including lncRNAs, transcription factor binding sites and m6A modification sites of lncRNAs, putatively translated open reading frames in lncRNAs) and steps of evaluating the effects of variations on the transcriptional regulation and modification of lncRNAs.

Key words

Long noncoding genes Single nucleotide polymorphism Transcriptional regulation Topologically associating domains RNA modification Small peptide 

Notes

Acknowledgments

This work was supported by National Natural Science Foundation of China (31701122).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Xiaowei Chen
    • 1
    • 2
  • Yajing Hao
    • 1
    • 3
  • Ya Cui
    • 1
    • 3
  • Zhen Fan
    • 1
    • 2
  • Runsheng Chen
    • 1
    • 4
    Email author
  1. 1.CAS Key Laboratory of RNA BiologyInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
  2. 2.Core Facility for Protein ResearchInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
  3. 3.University of Chinese Academy of SciencesBeijingChina
  4. 4.Research Network of Computational Biology, RNCBBeijingChina

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