Skip to main content
SpringerLink
Log in

LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes

  • Protocol
  • First Online:
Epitranscriptomics

Part of the book series: Methods in Molecular Biology ((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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145–166. https://doi.org/10.1146/annurev-biochem-051410-092902

    Article  CAS  PubMed  Google Scholar 

  2. Ulitsky I, Bartel David P (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154(1):26–46. https://doi.org/10.1016/j.cell.2013.06.020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Hu X, Feng Y, Zhang D, Zhao SD, Hu Z, Greshock J, Zhang Y, Yang L, Zhong X, Wang LP, Jean S, Li C, Huang Q, Katsaros D, Montone KT, Tanyi JL, Lu Y, Boyd J, Nathanson KL, Li H, Mills GB, Zhang L (2014) A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer. Cancer Cell 26(3):344–357. https://doi.org/10.1016/j.ccr.2014.07.009. S1535-6108(14)00300-6 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Pandey GK, Mitra S, Subhash S, Hertwig F, Kanduri M, Mishra K, Fransson S, Ganeshram A, Mondal T, Bandaru S, Ostensson M, Akyurek LM, Abrahamsson J, Pfeifer S, Larsson E, Shi L, Peng Z, Fischer M, Martinsson T, Hedborg F, Kogner P, Kanduri C (2014) The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation. Cancer Cell 26(5):722–737. https://doi.org/10.1016/j.ccell.2014.09.014. S1535-6108(14)00377-8 [pii]

    Article  CAS  PubMed  Google Scholar 

  5. Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, Davuluri RV, Nagy R, de la Chapelle A (2012) The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type. Proc Natl Acad Sci U S A 109(22):8646–8651. https://doi.org/10.1073/pnas.1205654109. 1205654109 [pii]

  6. Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Varnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnstrom K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P (2016) Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Cell 167(5):1369–1384. . S0092-8674(16)31322-8 [pii]. https://doi.org/10.1016/j.cell.2016.09.037

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Li S, Mason CE (2014) The pivotal regulatory landscape of RNA modifications. Annu Rev Genomics Hum Genet 15:127–150. https://doi.org/10.1146/annurev-genom-090413-025405

    Article  CAS  PubMed  Google Scholar 

  8. Harper JE, Miceli SM, Roberts RJ, Manley JL (1990) Sequence specificity of the human mRNA N6-adenosine methylase in vitro. Nucleic Acids Res 18(19):5735–5741

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, Cesarkas K, Jacob-Hirsch J, Amariglio N, Kupiec M, Sorek R, Rechavi G (2012) Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485(7397):201–206. https://doi.org/10.1038/nature11112. nature11112 [pii]

    Article  CAS  PubMed  Google Scholar 

  10. Anderson DM, Anderson KM, Chang CL, Makarewich CA, Nelson BR, McAnally JR, Kasaragod P, Shelton JM, Liou J, Bassel-Duby R, Olson EN (2015) A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell 160(4):595–606. https://doi.org/10.1016/j.cell.2015.01.009. S0092-8674(15)00010-0 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H (2014) The NHGRI GWAS catalog, a curated resource of SNP-trait associations. Nucleic Acids Res 42(Database issue):D1001–D1006. https://doi.org/10.1093/nar/gkt1229. gkt1229 [pii]

    Article  CAS  PubMed  Google Scholar 

  12. Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan, Shunmin He, Jianjun Luo, Runsheng Chen, (2016) LncVar: a database of genetic variation associated with long non-coding genes. Bioinformatics 33 (1):112–118

    Google Scholar 

  13. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841–842. https://doi.org/10.1093/bioinformatics/btq033. btq033 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170 btu170 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12(4):357–360. https://doi.org/10.1038/nmeth.3317. nmeth.3317 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9(9):R137. https://doi.org/10.1186/gb-2008-9-9-r137. gb-2008-9-9-r137 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111. https://doi.org/10.1093/bioinformatics/btp120. btp120 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Xie C, Yuan J, Li H, Li M, Zhao G, Bu D, Zhu W, Wu W, Chen R, Zhao Y (2014) NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res 42(Database issue):D98–D103. https://doi.org/10.1093/nar/gkt1222. gkt1222 [pii]

    Article  CAS  PubMed  Google Scholar 

  19. Mathelier A, Fornes O, Arenillas DJ, Chen CY, Denay G, Lee J, Shi W, Shyr C, Tan G, Worsley-Hunt R, Zhang AW, Parcy F, Lenhard B, Sandelin A, Wasserman WW (2016) JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res 44(D1):D110–D115. https://doi.org/10.1093/nar/gkv1176. gkv1176 [pii]

    Article  CAS  PubMed  Google Scholar 

  20. Teng L, He B, Wang J, Tan K (2015) 4DGenome: a comprehensive database of chromatin interactions. Bioinformatics 31(15):2560–2564. https://doi.org/10.1093/bioinformatics/btv158. btv158 [pii]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

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

Author information

Authors and Affiliations

  1. CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

    Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan & Runsheng Chen

  2. Core Facility for Protein Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

    Xiaowei Chen & Zhen Fan

  3. University of Chinese Academy of Sciences, Beijing, China

    Yajing Hao & Ya Cui

  4. Research Network of Computational Biology, RNCB, Beijing, China

    Runsheng Chen

Authors
  1. Xiaowei Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yajing Hao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ya Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhen Fan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Runsheng Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Runsheng Chen .

Editor information

Editors and Affiliations

  1. Department of Pathology, Yale University School of Medicine, New Haven, CT, USA

    Narendra Wajapeyee

  2. Yale Cancer Center, Yale University School of Medicine, New Haven, CT, USA

    Romi Gupta

Rights and permissions

Reprints and permissions

Copyright information

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

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Chen, X., Hao, Y., Cui, Y., Fan, Z., Chen, R. (2019). LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes. In: Wajapeyee, N., Gupta, R. (eds) Epitranscriptomics. Methods in Molecular Biology, vol 1870. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8808-2_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-8808-2_14

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8807-5

  • Online ISBN: 978-1-4939-8808-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation