Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Uniting ENCODE with genome-wide proteomics

Nature Biotechnology volume 30, pages 1065–1067 (2012)Cite this article

Subjects

An important goal of future omics research is to determine how the annotated regions of the genome control the production of protein isoforms.

What are the major points of synergy between ENCODE and C-HPP, and what can be gained by integrating the two data sets? Examples include the search for 'missing' proteins that have not been identified in proteomic studies, understanding the relationship of transcription-factor expression patterns to sets of protein variants, and defining the biochemical signatures of certain noncoding genomic regions and resulting protein modules. Despite the low abundance of most transcription factors, immunoprecipitation combined with high-sensitivity mass spectrometry platforms3 can be used to study how transcription factors mediate the formation of chromosomal loops and heterochromatin stability. The role of long noncoding RNAs, sequence-specific factors and histone modifications can also be analyzed by cell-based proteomics with top-down mass spectrometry4. Given that only one-third of protein-coding genes annotated in GENCODE have been validated by mass spectrometry analysis5, C-HPP will provide peptide evidence for newly identified coding loci3.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

Buy

All prices are NET prices.

Figure 1: Synergies to be achieved by uniting ENCODE and C-HPP.

References

  1. ENCODE Project Consortium. Nature 489, 57–74 (2012).

  2. Paik, Y.K. et al. Nat. Biotechnol. 30, 221–223 (2012).

    CAS  Article  Google Scholar 

  3. Sidoli, S. et al. J. Proteomics 75, 3419–3433 (2012).

    CAS  Article  Google Scholar 

  4. Tran, J.C. et al. Nature 480, 254–258 (2011).

    CAS  Article  Google Scholar 

  5. Harrow, J. et al. Genome Res. 22, 1760–1774 (2012).

    CAS  Article  Google Scholar 

  6. http://www.ensembl.org/, http://www.genecards.org/, http://www.nextprot.org/, http://gpmdb.thegpm.org/, http://www.peptideatlas.org/, http://www.proteinatlas.org/.

  7. Lundberg, E. et al. Mol. Syst. Biol. 6, 450 (2010).

    Article  Google Scholar 

  8. Germann, S. et al. J. Nucleic Acids. 2012, 269570 (2012).

    Article  Google Scholar 

  9. Califano, A. et al. Nat. Genet. 44, 841–847 (2012).

    CAS  Article  Google Scholar 

  10. Kauraniemi, P. et al. Cancer Res. 61, 8235–8240 (2001).

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Young-Ki Paik is in the Department of Integrated Omics for Biomedical Science, Yonsei Proteome Research Center, Yonsei University, Seoul, Korea, and,

    Young-Ki Paik

  2. William S. Hancock is in Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, USA, and World Class University Program, Yonsei University, Seoul, Korea.,

    William S Hancock

Authors
  1. Young-Ki Paik
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. William S Hancock
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Young-Ki Paik or William S Hancock.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Paik, YK., Hancock, W. Uniting ENCODE with genome-wide proteomics. Nat Biotechnol 30, 1065–1067 (2012). https://doi.org/10.1038/nbt.2416

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt.2416

Further reading

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing