Discovering Transcription Factor Noncoding RNA Targets Using ChIP-Seq Analysis

  • Vitalay FominEmail author
  • Carol PrivesEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2108)


Next generation sequencing enables large-scale analysis of mRNA expression (RNA-seq), genome variance (whole genome or exome), and transcription factor binding (ChIP-seq). Here we describe a method that allows the identification of transcription factor-binding sites in the vicinity of nonprotein-coding genes.

Key words

ChIP-seq p53 Noncoding Transcription factor Next generation sequencing 


  1. 1.
    Djebali S, Davis CA, Merkel A et al (2012) Landscape of transcription in human cells. Nature 489:101–108. Scholar
  2. 2.
    Pertea M (2012) The human transcriptome: an unfinished story. Genes 3:344–360. Scholar
  3. 3.
    Hu WL, Jin L, Xu A et al (2018) GUARDIN is a p53-responsive long non-coding RNA that is essential for genomic stability. Nat Cell Biol 20:492–502. Scholar
  4. 4.
    Engreitz JM, Pandya-Jones A, McDonel P et al (2013) The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341:1237973. Scholar
  5. 5.
    Fang Y, Fullwood MJ (2016) Roles, functions, and mechanisms of long non-coding RNAs in cancer. Genomics Proteomics Bioinformatics 14:42–54. Scholar
  6. 6.
    Gloss BS, Dinger ME (2016) The specificity of long noncoding RNA expression. Biochim Biophys Acta 1859:16–22. Scholar
  7. 7.
    Menendez D, Nguyen T-A, Freudenberg JM et al (2013) Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells. Nucleic Acids Res 41:7286–7301. Scholar
  8. 8.
    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. Scholar
  9. 9.
    Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. Scholar
  10. 10.
    Heinz S, Benner C, Spann N et al (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38:576–589CrossRefGoogle Scholar
  11. 11.
    Robinson JT, Thorvaldsdóttir H, Winckler W et al (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26. Scholar
  12. 12.
    Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions. Nat Rev Genet 13(12):840–852. Scholar
  13. 13.
    Landt SG, Marinov GK, Kundaje A et al (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22:1813–1831. Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Department of Biological SciencesColumbia UniversityNew YorkUSA

Personalised recommendations