Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins

Rafiee, Mahmoud Reza; Girardot, Charles; Sigismondo, Gianluca; Krijgsveld, Jeroen

doi:10.1016/j.molcel.2016.09.019

Cited by 89 publications

(121 citation statements)

References 51 publications

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“…Downregulation of TRIM24 expression in human ES cells leads to spontaneous differentiation, which is in contrast to human breast cancer cells where TRIM24 depletion induces spontaneous apoptosis . Moreover, TRIM24 converges with Oct‐3/4, Sox2, and NANOG on multiple enhancers and suppresses the expression of developmental genes to support the pluripotent state of stem cells …”

Section: The Engagement Of Specific Trims In Stem Cell Maintenancementioning

confidence: 99%

The role of TRIM family proteins in the regulation of cancer stem cell self-renewal

et al. 2019

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The tripartite-motif (TRIM) family of proteins represents one of the largest classes of putative single protein RING-finger E3 ubiquitin ligases. The members of this family are characterized by an N-terminal TRIM motif containing one RING-finger domain, one or two zinc-finger domains called B boxes (B1 box and B2 box), and a coiled-coil region.The TRIM motif can be found in isolation or in combination with a variety of C-terminal domains, and based on C-terminus, TRIM proteins are classified into 11 distinct groups.Because of the complex nature of TRIM proteins, they are implicated in a variety of cellular functions and biological processes, including regulation of cell proliferation, cell division and developmental processes, cancer transformation, regulation of cell metabolism, autophagocytosis, modification of chromatin status, regulation of gene transcription, post-translational modifications, and interactions with pathogens. Here, we demonstrate the specific activities of TRIM family proteins that contribute to the cancer stem cell phenotype. A growing body of evidence demonstrates that several TRIM members guarantee the acquisition of stem cell properties and the ability to sustain stem-like phenotype by cancer cells using distinct mechanisms. For other members, further work is needed to understand their full contribution to stem cell self-renewal.Identification of TRIM proteins that possess the potential to serve as therapeutic targets may result in the development of new therapeutic strategies. Finally, these strategies may result in the disruption of the machinery of stemness acquisition, which may prevent tumor growth, progression, and overcome the resistance to anticancer therapies. K E Y W O R D Scancer, pluripotency, RING, self-renewal, stem cells, TRIM

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Section: The Engagement Of Specific Trims In Stem Cell Maintenancementioning

confidence: 99%

The role of TRIM family proteins in the regulation of cancer stem cell self-renewal

et al. 2019

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“…Overall, this study by Rafiee et al () presents a very useful improvement in the methodological toolbox available for the selective purification and identification of protein complexes and protein interaction networks associated with chromatin. The ChIP‐SICAP method offers several specific advantages: (i) it allows selective and reproducible isolation of chromatin‐associated proteins, together with the cognate, bound DNA element, (ii) it offers the possibility to distinguish between protein interactions taking place either, on or off, chromatin, and (iii) it facilitates combining proteomics analysis and ChIP‐seq in a single experiment.…”

Section: Sicap Methodsmentioning

confidence: 97%

“…In their recent work, Rafiee et al () describe a new method for the selective isolation of chromatin‐associated proteins (SICAP), which improves selectivity. The method involves ChIP of DNA‐protein complexes, combined with biotin tagging of DNA, to allow the specific isolation of DNA‐bound proteins on streptavidin beads, followed by MS‐based protein identification (Fig ).…”

Section: Sicap Methodsmentioning

confidence: 99%

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Unlocking the chromatin code by deciphering protein– DNA interactions

Bensaddek

2016

Molecular Systems Biology

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Characterizing the composition of protein complexes bound to different genomic loci is essential for advancing our mechanistic understanding of transcriptional regulation. In their recent study, Krijgsveld and colleagues (Rafiee et al, 2016) report ChIP‐SICAP, a powerful tool for deciphering the chromatin proteome by combining chromatin immunoprecipitation, selective isolation of chromatin‐associated proteins and mass spectrometry.

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“…Crosslinking allows for the preservation of weak and transient interactions during harsh steps, such as sonication and stringent washing and has been optimized for different applications [16, 17, 18, 19]. From this, numerous methods have been developed that allow for proteomic analysis at specific genomic regions.…”

Section: Capturing Chromatin Proteins For Proteomic Analysismentioning

confidence: 99%

Unravelling the biology of chromatin in health and cancer using proteomic approaches

Eubanks

Dayebgadoh

Liu

et al. 2017

Expert Review of Proteomics

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Introduction: Chromatin remodeling complexes play important roles in the control of genome regulation in both normal and diseased states, and are therefore critical components for the regulation of epigenetic states in cells. Given the role epigenetics plays in cancer, for example, chromatin remodeling complexes are routinely targeted for therapeutic intervention. Areas covered: Protein mass spectrometry and proteomics are powerful technologies used to study and understand chromatin remodeling. While impressive progress has been made in this area, there remain significant challenges in the application of proteomic technologies to the study of chromatin remodeling. As parts of large multisubunit complexes that can be heavily modified with dynamic post-translational modifications, challenges in the study of chromatin remodeling complexes include defining the content, determining the regulation, and studying the dynamics of the complexes under different cellular states. Expert Commentary: Important considerations in the study of chromatin remodeling complexes include the complexity of sample preparation, the choice of proteomic methods for the analysis of samples, and data analysis challenges. Continued research in these three areas promise to yield even greater insights into the biology of chromatin remodeling and epigenetics and the dynamics of these systems in human health and cancer.

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Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins

Cited by 89 publications

References 51 publications

The role of TRIM family proteins in the regulation of cancer stem cell self-renewal

The role of TRIM family proteins in the regulation of cancer stem cell self-renewal

Unlocking the chromatin code by deciphering protein– DNA interactions

Unravelling the biology of chromatin in health and cancer using proteomic approaches

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