Skip to main content
SpringerLink
Log in

Identification of Transcription Factor-Binding Sites in the Mouse FOXO1 Promoter

  • Protocol
  • First Online:
FOXO Transcription Factors

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1890))

Abstract

One critical determinant of levels of gene expression is binding of transcription factors to cognate DNA sequences in promoter and enhancer regions of target genes. Transcription factors are DNA-binding proteins to which transcriptional co-regulators are bound, ultimately resulting in histone modifications that change chromatin structure to regulate transcription. Examples of transcription factors include hormone-activated transcription factors such as the glucocorticoid receptor, transcription factors regulated by cell surface receptors such as FOXO1 and Smad2/Smad3, and many others. Promoter regions typically contain multiple, diverse transcription factor-binding sites. Binding sites for cell-type-specific transcription factors involved in cell fate determination such as Runx2, MyoD, or myogenin are frequently observed. Promoter regions are located within ~2 kb upstream of the transcriptional start site, whereas enhancers may be located at some distance from promoter sequences and exert long-range effects. Here, we will discuss classical and emerging technologies by which one can understand the role of binding of specific transcription factors in regulation of transcription of FOXO genes.

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 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
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. Kadmiel M, Cidlowski JA (2013) Glucocorticoid receptor signaling in health and disease. Trends Pharmacol Sci 34:518–530. https://doi.org/10.1016/j.tips.2013.07.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Weikum ER, Knuesel MT, Ortlund EA, Yamamoto KR (2017) Glucocorticoid receptor control of transcription: precision and plasticity via allostery. Nat Rev Mol Cell Biol 18:159–174. https://doi.org/10.1038/nrm.2016.152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. de Jaime-Soguero A, Abreu de Oliveira WA, Lluis F (2018) The Pleiotropic effects of the canonical Wnt pathway in early development and pluripotency. Genes (Basel) 9(2). pii: E93. https://doi.org/10.3390/genes9020093

  4. Masek J, Andersson ER (2017) The developmental biology of genetic Notch disorders. Development 144:1743–1763. https://doi.org/10.1242/dev.148007

    Article  CAS  PubMed  Google Scholar 

  5. Parchure A, Vyas N, Mayor S (2018) Wnt and hedgehog: secretion of lipid-modified morphogens. Trends Cell Biol 28:157–170. https://doi.org/10.1016/j.tcb.2017.10.003

    Article  CAS  PubMed  Google Scholar 

  6. Siebel C, Lendahl U (2017) Notch signaling in development, tissue homeostasis, and disease. Physiol Rev 97:1235–1294. https://doi.org/10.1152/physrev.00005.2017

    Article  CAS  PubMed  Google Scholar 

  7. Sarfstein R, Werner H (2013) Minireview: nuclear insulin and insulin-like growth factor-1 receptors: a novel paradigm in signal transduction. Endocrinology 154:1672–1679. https://doi.org/10.1210/en.2012-2165

    Article  CAS  PubMed  Google Scholar 

  8. Qin W, Pan J, Qin Y, Lee DN, Bauman WA, Cardozo C (2014) Identification of functional glucocorticoid response elements in the mouse FoxO1 promoter. Biochem Biophys Res Commun 450:979–983. https://doi.org/10.1016/j.bbrc.2014.06.080

    Article  CAS  PubMed  Google Scholar 

  9. Zhao W, Pan J, Wang X, Wu Y, Bauman WA, Cardozo CP (2008) Expression of the muscle atrophy factor muscle atrophy F-box is suppressed by testosterone. Endocrinology 149:5449–5460. https://doi.org/10.1210/en.2008-0664

    Article  CAS  PubMed  Google Scholar 

  10. Wu Y et al (2007) Identification of androgen response elements in the insulin-like growth factor I upstream promoter. Endocrinology 148:2984–2993. https://doi.org/10.1210/en.2006-1653

    Article  CAS  PubMed  Google Scholar 

  11. Wu Y et al (2007) Identification of androgen response elements in the IGF-1 upstream promoter. Endocrinology 148:2984–2993

    Article  CAS  PubMed  Google Scholar 

  12. Liu XH, De Gasperi R, Bauman WA, Cardozo CP (2018) Nandrolone-induced nuclear accumulation of MyoD protein is mediated by Numb, a Notch inhibitor, in C2C12 myoblasts. Physiol Rep 6. https://doi.org/10.14814/phy2.13520

  13. Wu Y, Ruggiero CL, Bauman WA, Cardozo C (2013) Ankrd1 is a transcriptional repressor for the androgen receptor that is downregulated by testosterone. Biochem Biophys Res Commun 437:355–360. https://doi.org/10.1016/j.bbrc.2013.06.079

    Article  CAS  PubMed  Google Scholar 

  14. Liu XH et al (2013) Androgens up-regulate transcription of the Notch inhibitor Numb in C2C12 myoblasts via Wnt/beta-catenin signaling to T cell factor elements in the Numb promoter. J Biol Chem 288:17990–17998. https://doi.org/10.1074/jbc.M113.478487

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Kim TK, Shiekhattar R (2015) Architectural and functional commonalities between enhancers and promoters. Cell 162:948–959. https://doi.org/10.1016/j.cell.2015.08.008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 13:840–852. https://doi.org/10.1038/nrg3306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Ghavi-Helm Y, Zhao B, Furlong EE (2016) Chromatin immunoprecipitation for analyzing transcription factor binding and histone modifications in drosophila. Methods Mol Biol 1478:263–277. https://doi.org/10.1007/978-1-4939-6371-3_16

    Article  CAS  PubMed  Google Scholar 

  18. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680. https://doi.org/10.1038/nrg2641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Yan H, Tian S, Slager SL, Sun Z (2016) ChIP-seq in studying epigenetic mechanisms of disease and promoting precision medicine: progresses and future directions. Epigenomics 8:1239–1258. https://doi.org/10.2217/epi-2016-0053

    Article  CAS  PubMed  Google Scholar 

  20. Biterge B, Schneider R (2014) Histone variants: key players of chromatin. Cell Tissue Res 356:457–466. https://doi.org/10.1007/s00441-014-1862-4

    Article  CAS  PubMed  Google Scholar 

  21. Graff J, Tsai LH (2013) Histone acetylation: molecular mnemonics on the chromatin. Nat Rev Neurosci 14:97–111. https://doi.org/10.1038/nrn3427

    Article  CAS  PubMed  Google Scholar 

  22. Tessarz P, Kouzarides T (2014) Histone core modifications regulating nucleosome structure and dynamics. Nat Rev Mol Cell Biol 15:703–708. https://doi.org/10.1038/nrm3890

    Article  CAS  PubMed  Google Scholar 

  23. Baek S, Sung MH (2016) Genome-scale analysis of cell-specific regulatory codes using nuclear enzymes. Methods Mol Biol 1418:225–240. https://doi.org/10.1007/978-1-4939-3578-9_12

    Article  PubMed  PubMed Central  Google Scholar 

  24. Degner JF et al (2012) DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482:390–394. https://doi.org/10.1038/nature10808

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Filichkin SA, Megraw M (2017) DNase I SIM: a simplified in-nucleus method for DNase I hypersensitive site sequencing. Methods Mol Biol 1629:141–154. https://doi.org/10.1007/978-1-4939-7125-1_10

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by VA Rehabilitation Research and Development Grant B-2020-C.

Author information

Authors and Affiliations

  1. Center for the Medical Consequences of Spinal Cord Injury, James J Peters Medical Center, Bronx, NY, USA

    Christopher P. Cardozo

  2. Icahn School of Medicine at Mount Sinai, New York, NY, USA

    Christopher P. Cardozo

Authors
  1. Christopher P. Cardozo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Christopher P. Cardozo .

Editor information

Editors and Affiliations

  1. Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Madrid, Spain

    Wolfgang Link

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

Cardozo, C.P. (2019). Identification of Transcription Factor-Binding Sites in the Mouse FOXO1 Promoter. In: Link, W. (eds) FOXO Transcription Factors. Methods in Molecular Biology, vol 1890. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-8900-3_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-8900-3_3

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-8899-0

  • Online ISBN: 978-1-4939-8900-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation