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Discovering Transcription Factor Noncoding RNA Targets Using ChIP-Seq Analysis

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Immune Mediators in Cancer

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2108))

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Abstract

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.

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References

  1. Djebali S, Davis CA, Merkel A et al (2012) Landscape of transcription in human cells. Nature 489:101–108. https://doi.org/10.1038/nature11233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Pertea M (2012) The human transcriptome: an unfinished story. Genes 3:344–360. https://doi.org/10.3390/genes3030344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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. https://doi.org/10.1038/s41556-018-0066-7

    Article  CAS  PubMed  Google Scholar 

  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. https://doi.org/10.1126/science.1237973

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Fang Y, Fullwood MJ (2016) Roles, functions, and mechanisms of long non-coding RNAs in cancer. Genomics Proteomics Bioinformatics 14:42–54. https://doi.org/10.1016/j.gpb.2015.09.006

    Article  PubMed  PubMed Central  Google Scholar 

  6. Gloss BS, Dinger ME (2016) The specificity of long noncoding RNA expression. Biochim Biophys Acta 1859:16–22. https://doi.org/10.1016/j.bbagrm.2015.08.005

    Article  CAS  PubMed  Google Scholar 

  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. https://doi.org/10.1093/nar/gkt504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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 38:576–589

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Robinson JT, Thorvaldsdóttir H, Winckler W et al (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26. https://doi.org/10.1038/nbt.1754

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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. https://doi.org/10.1038/nrg3306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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. https://doi.org/10.1101/gr.136184.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Correspondence to Vitalay Fomin or Carol Prives .

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Fomin, V., Prives, C. (2020). Discovering Transcription Factor Noncoding RNA Targets Using ChIP-Seq Analysis. In: Vancurova, I., Zhu, Y. (eds) Immune Mediators in Cancer. Methods in Molecular Biology, vol 2108. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0247-8_26

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  • DOI: https://doi.org/10.1007/978-1-0716-0247-8_26

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0246-1

  • Online ISBN: 978-1-0716-0247-8

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