Skip to main content
SpringerLink
Log in

Mass spectrometry-based proteomic capture of proteins bound to the MACC1 promoter in colon cancer

  • Research Paper
  • Published:
Clinical & Experimental Metastasis Aims and scope Submit manuscript

A Correction to this article was published on 04 September 2020

This article has been updated

Abstract

MACC1 (metastasis associated in colon cancer 1) is a key driver that induces metastasis in colon cancer. However, the mechanisms by which MACC1 expression is transcriptionally regulated and the factors enriched at the MACC1 promoter remain largely unknown. The binding of proteins to specific DNA sites in the genome is a major determinant of genomic maintenance and the regulation of specific genes. The study herein utilized two methods to study the binding proteins of the MACC1 promoter region in colon cancer. Specifically, we adopted CRISPR-based chromatin affinity purification with mass spectrometry (CRISPR-ChAP-MS) and a biotin-streptavidin pulldown assay coupled with MS to identify the specific proteome bound to the MACC1 promoter in two colon cell lines with different metastatic potential. A total of 24 proteins were identified by CRISPR-ChAP-MS as binding to the MACC1 promoter, among which c-JUN was validated by ChIP-PCR. A total of 739 binding protein candidates were identified by biotin-streptavidin pulldown assays coupled with MS, of which HNF4G and PAX6 were validated and compared for their binding to the same promoter sites in the two cell lines. Our studies suggest distinctive proteomic factors associated with the MACC1 promoter in colon cells with different metastatic potential. The dynamic regulatory factors accumulated at the promoter of MACC1 may provide novel insights into the regulatory mechanisms of MACC1 transcription.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Change history

  • 04 September 2020

    In the original publication of the article, Acknowledgements section was published incorrectly. The correct Acknowledgements is given in this Correction.

References

  1. Wierer M, Mann M (2016) Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes. Hum Mol Genet 25(R2):R106–r114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Byrum SD et al (2012) ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus. Cell Rep 2(1):198–205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Byrum SD, Taverna SD, Tackett AJ (2013) Purification of a specific native genomic locus for proteomic analysis. Nucleic Acids Res 41(20):e195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Dejardin J, Kingston RE (2009) Purification of proteins associated with specific genomic Loci. Cell 136(1):175–186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Kappei D et al (2013) HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment. Embo J 32(12):1681–1701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Mittler G, Butter F, Mann M (2009) A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements. Genome Res 19(2):284–293

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Waldrip ZJ et al (2014) A CRISPR-based approach for proteomic analysis of a single genomic locus. Epigenetics 9(9):1207–1211

    Article  PubMed  PubMed Central  Google Scholar 

  8. Viturawong T et al (2013) A DNA-centric protein interaction map of ultraconserved elements reveals contribution of transcription factor binding hubs to conservation. Cell Rep 5(2):531–545

    Article  CAS  PubMed  Google Scholar 

  9. Butter F et al (2012) Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding. PLoS Genet 8(9):e1002982

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Spruijt CG et al (2013) Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152(5):1146–1159

    Article  CAS  PubMed  Google Scholar 

  11. Fujita T, Fujii H (2013) Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR. Biochem Biophys Res Commun 439(1):132–136

    Article  CAS  PubMed  Google Scholar 

  12. Fujita T, Fujii H (2014) Identification of proteins associated with an IFNgamma-responsive promoter by a retroviral expression system for enChIP using CRISPR. PLoS ONE 9(7):e103084

    Article  PubMed  PubMed Central  Google Scholar 

  13. Hamidian A et al (2018) Promoter-associated proteins of EPAS1 identified by enChIP-MS—a putative role of HDX as a negative regulator. Biochem Biophys Res Commun 499(2):291–298

    Article  CAS  PubMed  Google Scholar 

  14. Mochizuki Y et al (2018) Combinatorial CRISPR/Cas9 approach to elucidate a far-upstream enhancer complex for tissue-specific Sox9 expression. Dev Cell 46(6):794–806.e6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Stein U et al (2009) MACC1, a newly identified key regulator of HGF-MET signaling, predicts colon cancer metastasis. Nat Med 15(1):59–67

    Article  CAS  PubMed  Google Scholar 

  16. Radhakrishnan H et al (2018) MACC1-the first decade of a key metastasis molecule from gene discovery to clinical translation. Cancer Metastasis Rev 37(4):805–820

    Article  CAS  PubMed  Google Scholar 

  17. Guo T et al (2017) YB-1 regulates tumor growth by promoting MACC1/c-Met pathway in human lung adenocarcinoma. Oncotarget 8(29):48110–48125

    Article  PubMed  PubMed Central  Google Scholar 

  18. Juneja M et al (2013) Promoter identification and transcriptional regulation of the metastasis gene MACC1 in colorectal cancer. Mol Oncol 7(5):929–943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kuo IY et al (2014) Low SOX17 expression is a prognostic factor and drives transcriptional dysregulation and esophageal cancer progression. Int J Cancer 135(3):563–573

    Article  CAS  PubMed  Google Scholar 

  20. Deng WG et al (2006) Melatonin suppresses macrophage cyclooxygenase-2 and inducible nitric oxide synthase expression by inhibiting p52 acetylation and binding. Blood 108(2):518–524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Horlbeck MA et al (2016) Nucleosomes impede Cas9 access to DNA in vivo and in vitro. Elife 5:e12677

    Article  PubMed  PubMed Central  Google Scholar 

  22. Foulds CE et al (2013) Proteomic analysis of coregulators bound to ERalpha on DNA and nucleosomes reveals coregulator dynamics. Mol Cell 51(2):185–199

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Sharma NL et al (2014) The ETS family member GABPalpha modulates androgen receptor signalling and mediates an aggressive phenotype in prostate cancer. Nucleic Acids Res 42(10):6256–6269

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Li CG, Eccles MR (2012) PAX genes in cancer; friends or foes? Front Genet 3:6

    PubMed  PubMed Central  Google Scholar 

  25. Mascarenhas JB et al (2009) PAX6 is expressed in pancreatic cancer and actively participates in cancer progression through activation of the MET tyrosine kinase receptor gene. J Biol Chem 284(40):27524–27532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Nemlich Y et al (2018) ADAR1-mediated regulation of melanoma invasion. Nat Commun 9(1):2154

    Article  PubMed  PubMed Central  Google Scholar 

  27. Li Y et al (2014) PAX6, a novel target of microRNA-7, promotes cellular proliferation and invasion in human colorectal cancer cells. Dig Dis Sci 59(3):598–606

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank the State Key Basic Research Development Plan (2011CB910700 microenvironmental proteomics of solid tumors) and the Teacher Research Fund of Central South University. We also thank the Department of Pathology, Xiangya Hospital, Central South University for technical support.

Author information

Author notes

  1. Yahui Huang and Yi Xiang have contributed equally to this work and should be considered co-first authors.

Authors and Affiliations

  1. Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China

    Yahui Huang, Zhongpeng Xie, Yuxiang Cai, Qiongzhi Yang & Qiongqiong He

  2. School of Basic Medical Sciences, Central South University, Changsha, Hunan, People’s Republic of China

    Yahui Huang, Yi Xiang, Zhongpeng Xie, Yuxiang Cai, Qiongzhi Yang & Qiongqiong He

  3. NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China

    Huichao Huang, Zhuchu Chen & Zhefeng Xiao

  4. Department of Pathology, Xuchang Central Hospital, Henan University of Science and Technology, Xuchang, Henan, People’s Republic of China

    Yahui Huang

  5. Department of Pathology, Hainan General Hospital, Haikou, Hainan, People’s Republic of China

    Zhongpeng Xie

Authors
  1. Yahui Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yi Xiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhongpeng Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yuxiang Cai
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Qiongzhi Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Huichao Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zhuchu Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Zhefeng Xiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Qiongqiong He
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

YH, ZX and QH conceived and designed the experiments and wrote the manuscript; YH, ZX and YX performed the experiments and analyzed the data; and YC, QY, HH and ZC evaluated the experimental data and contributed to the revision of the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Zhefeng Xiao or Qiongqiong He.

Ethics declarations

Conflict of interest

No potential conflict of interest was reported.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 70 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Huang, Y., Xiang, Y., Xie, Z. et al. Mass spectrometry-based proteomic capture of proteins bound to the MACC1 promoter in colon cancer. Clin Exp Metastasis 37, 477–487 (2020). https://doi.org/10.1007/s10585-020-10045-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10585-020-10045-z

Keywords

Search

Navigation