1
|
MacKenzie TMG, Cisneros R, Maynard RD, Snyder MP. Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome. Cells 2023; 12:1860. [PMID: 37508524 PMCID: PMC10377898 DOI: 10.3390/cells12141860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
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.
Collapse
Affiliation(s)
| | - Rocío Cisneros
- Sarafan ChEM-H/IMA Postbaccalaureate Fellow in Target Discovery, Stanford University, Stanford, CA 94305, USA
| | - Rajan D Maynard
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
3
|
Guillen-Ahlers H, Rao PK, Perumalla DS, Montoya MJ, Jadhav AYL, Shortreed MR, Smith LM, Olivier M. Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells. J Vis Exp 2018. [PMID: 29912191 DOI: 10.3791/57140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The hybridization capture of chromatin-associated proteins for proteomics (HyCCAPP) technology was initially developed to uncover novel DNA-protein interactions in yeast. It allows analysis of a target region of interest without the need for prior knowledge about likely proteins bound to the target region. This, in theory, allows HyCCAPP to be used to analyze any genomic region of interest, and it provides sufficient flexibility to work in different cell systems. This method is not meant to study binding sites of known transcription factors, a task better suited for Chromatin Immunoprecipitation (ChIP) and ChIP-like methods. The strength of HyCCAPP lies in its ability to explore DNA regions for which there is limited or no knowledge about the proteins bound to it. It can also be a convenient method to avoid biases (present in ChIP-like methods) introduced by protein-based chromatin enrichment using antibodies. Potentially, HyCCAPP can be a powerful tool to uncover truly novel DNA-protein interactions. To date, the technology has been predominantly applied to yeast cells or to high copy repeat sequences in mammalian cells. In order to become the powerful tool we envision, HyCCAPP approaches need to be optimized to efficiently capture single-copy loci in mammalian cells. Here, we present our adaptation of the initial yeast HyCCAPP capture protocol to human cell lines, and show that single-copy chromatin regions can be efficiently isolated with this modified protocol.
Collapse
Affiliation(s)
- Hector Guillen-Ahlers
- Department of Genetics, Texas Biomedical Research Institute; Department of Internal Medicine-Molecular Medicine, Wake Forest University School of Medicine
| | - Prahlad K Rao
- Department of Genetics, Texas Biomedical Research Institute
| | | | | | | | | | | | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute; Department of Internal Medicine-Molecular Medicine, Wake Forest University School of Medicine;
| |
Collapse
|
5
|
Guillen-Ahlers H, Rao PK, Levenstein ME, Kennedy-Darling J, Perumalla DS, Jadhav AYL, Glenn JP, Ludwig-Kubinski A, Drigalenko E, Montoya MJ, Göring HH, Anderson CD, Scalf M, Gildersleeve HIS, Cole R, Greene AM, Oduro AK, Lazarova K, Cesnik AJ, Barfknecht J, Cirillo LA, Gasch AP, Shortreed MR, Smith LM, Olivier M. HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics 2016; 107:267-73. [PMID: 27184763 DOI: 10.1016/j.ygeno.2016.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 11/30/2022]
Abstract
Currently available methods for interrogating DNA-protein interactions at individual genomic loci have significant limitations, and make it difficult to work with unmodified cells or examine single-copy regions without specific antibodies. In this study, we describe a physiological application of the Hybridization Capture of Chromatin-Associated Proteins for Proteomics (HyCCAPP) methodology we have developed. Both novel and known locus-specific DNA-protein interactions were identified at the ENO2 and GAL1 promoter regions of Saccharomyces cerevisiae, and revealed subgroups of proteins present in significantly different levels at the loci in cells grown on glucose versus galactose as the carbon source. Results were validated using chromatin immunoprecipitation. Overall, our analysis demonstrates that HyCCAPP is an effective and flexible technology that does not require specific antibodies nor prior knowledge of locally occurring DNA-protein interactions and can now be used to identify changes in protein interactions at target regions in the genome in response to physiological challenges.
Collapse
Affiliation(s)
- Hector Guillen-Ahlers
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Prahlad K Rao
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Mark E Levenstein
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | | | - Danu S Perumalla
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Avinash Y L Jadhav
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Jeremy P Glenn
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Amy Ludwig-Kubinski
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Eugene Drigalenko
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Maria J Montoya
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Harald H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Corianna D Anderson
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | | | - Regina Cole
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Alexandra M Greene
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Akua K Oduro
- Department of Cell Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Katarina Lazarova
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Jared Barfknecht
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Lisa A Cirillo
- Department of Cell Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Audrey P Gasch
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | | | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| |
Collapse
|