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Proximity labeling techniques to study chromatin.

Front. Genet. 11:450 (2020)
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Open Access Gold
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Mammals contain over 200 different cell types, yet nearly all have the same genomic DNA sequence. It is a key question in biology how the genetic instructions in DNA are selectively interpreted by cells to specify various transcriptional programs and therefore cellular identity. The structural and functional organization of chromatin governs the transcriptional state of individual genes. To understand how genomic loci adopt different levels of gene expression, it is critical to characterize all local chromatin factors as well as long-range interactions in the 3D nuclear compartment. Much of our current knowledge regarding protein interactions in a chromatin context is based on affinity purification of chromatin components coupled to mass spectrometry (AP-MS). AP-MS has been invaluable to map strong protein-protein interactions in the nucleus. However, the interaction is detected after cell lysis and biochemical enrichment, allowing for loss or gain of false positive or negative interaction partners. Recently, proximity-dependent labeling methods have emerged as powerful tools for studying chromatin in its native context. These methods take advantage of engineered enzymes that are fused to a chromatin factor of interest and can directly label all factors in proximity. Subsequent pull-down assays followed by mass spectrometry or sequencing approaches provide a comprehensive snapshot of the proximal chromatin interactome. By combining this method with dCas9, this approach can also be extended to study chromatin at specific genomic loci. Here, we review and compare current proximity-labeling approaches available for studying chromatin, with a particular focus on new emerging technologies that can provide important insights into the transcriptional and chromatin interaction networks essential for cellular identity.
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Publication type Article: Journal article
Document type Review
Keywords Protein-protein Interactions ; Proxisome ; Bioid ; Apex2 ; Dcas9 ; Chip ; Affinity Purification ; Mass Spectrometry; Promiscuous Protein Biotinylation; Engineered Ascorbate Peroxidase; Biotin Holoenzyme Synthetase; In-vivo Biotinylation; Affinity Purification; Mass-spectrometry; Cross-linking; Living Cells; Ku Protein; Bira Gene
ISSN (print) / ISBN 1664-8021
e-ISSN 1664-8021
Quellenangaben Volume: 11, Issue: , Pages: , Article Number: 450 Supplement: ,
Publisher Frontiers
Publishing Place Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
Reviewing status Peer reviewed