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

Huang, Ya‐Hui; Xiang, Yong‐Bing; Xie, Zheng; Cai, Yuxiang; Yang, Qiongzhi; Huang, Huichao; Chen, Zhuchu; Xiao, Zhefeng; He, Qiaojun

doi:10.1007/s10585-020-10045-z

Cited by 6 publications

(5 citation statements)

References 26 publications

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“…MACC1 expression induced metastasis of colon cancer, and the binding of HNF4G and PAX6 to the promoter was verified. The proteins associated with MACC1 promoter binding were different in colon cancer cells with different metastatic potentials ( 152 ).…”

Section: Using Novel Crispr/cas 9 Technology To Explore Other Areas O...mentioning

confidence: 99%

Application of CRISPR-Cas9 gene editing technology in basic research, diagnosis and treatment of colon cancer

Meng

Nan

et al. 2023

Front. Endocrinol.

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Colon cancer is the fourth leading cause of cancer death worldwide, and its progression is accompanied by a complex array of genetic variations. CRISPR/Cas9 can identify new drug-resistant or sensitive mutations in colon cancer, and can use gene editing technology to develop new therapeutic targets and provide personalized treatments, thereby significantly improving the treatment of colon cancer patients. CRISPR/Cas9 systems are driving advances in biotechnology. RNA-directed Cas enzymes have accelerated the pace of basic research and led to clinical breakthroughs. This article reviews the rapid development of CRISPR/Cas in colon cancer, from gene editing to transcription regulation, gene knockout, genome-wide CRISPR tools, therapeutic targets, stem cell genomics, immunotherapy, metabolism-related genes and inflammatory bowel disease. In addition, the limitations and future development of CRISPR/Cas9 in colon cancer studies are reviewed. In conclusion, this article reviews the application of CRISPR-Cas9 gene editing technology in basic research, diagnosis and treatment of colon cancer.

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Section: Using Novel Crispr/cas 9 Technology To Explore Other Areas O...mentioning

confidence: 99%

Application of CRISPR-Cas9 gene editing technology in basic research, diagnosis and treatment of colon cancer

Meng

Nan

et al. 2023

Front. Endocrinol.

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“…This observation highlights the need to carefully design the sgRNA and perform control experiments to determine off-target binding and the impact of chromatin state on target locus enrichment. A subsequent study from an independent research group utilized CRISPR-ChAP-MS in two colon cancer lines with varying degrees of metastatic potential to study the promoter of MACC1, a metastasis-associated gene [161]. Researchers also utilized a biotinylated DNA probe representing 500 bp of the promoter region to identify potential regulatory proteins.…”

Section: Crispr-chap-msmentioning

confidence: 99%

Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome

MacKenzie

Cisneros

Maynard

et al. 2023

Cells

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A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long‑range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP‑Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a ‘reverse-ChIP’ approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a ‘reverse-ChIP’ technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens.

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“…Huang and collaborators exploited the CRISPR-ChAP-MS technique to identify proteins interacting with MACC1 promoter. They use the catalytically inactive 3xFLAG tagged dCas9 along with a gRNA to target and isolate the promoter region of the MACC1 gene . The c-JUN transcription factor was found physically bound to the MACC1 promoter and able to upregulate its expression.…”

Section: Crispr-based Chromatin Affinity Purification–mass Spectromet...mentioning

confidence: 99%

Protein–DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era

et al. 2021

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The fields of application of functional proteomics are not limited to the study of protein–protein interactions; they also extend to those involving protein complexes that bind DNA or RNA. These interactions affect fundamental processes such as replication, transcription, and repair in the case of DNA, as well as transport, translation, splicing, and silencing in the case of RNA. Analytical or preparative experimental approaches, both in vivo and in vitro, have been developed to isolate and identify DNA/RNA binding proteins by exploiting the advantage of the affinity shown by these proteins toward a specific oligonucleotide sequence. The present review proposes an overview of the approaches most commonly employed in proteomics applications for the identification of nucleic acid-binding proteins, such as affinity purification (AP) protocols, EMSA, chromatin purification methods, and CRISPR-based chromatin affinity purification, which are generally associated with mass spectrometry methodologies for the unbiased protein identification.

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

Cited by 6 publications

References 26 publications

Application of CRISPR-Cas9 gene editing technology in basic research, diagnosis and treatment of colon cancer

Application of CRISPR-Cas9 gene editing technology in basic research, diagnosis and treatment of colon cancer

Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome

Protein–DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era

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